// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Clemens Groepl, Chris Bielow $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_MAPMATCHING_FEATUREGROUPINGALGORITHM_H
#define OPENMS_ANALYSIS_MAPMATCHING_FEATUREGROUPINGALGORITHM_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/ConsensusMap.h>

namespace OpenMS
{

  /**
      @brief Base class for all feature grouping algorithms

      These algorithms group corresponding features in one map or across maps.
  */
  class OPENMS_DLLAPI FeatureGroupingAlgorithm :
    public DefaultParamHandler
  {
public:
    /// Default constructor
    FeatureGroupingAlgorithm();

    /// Destructor
    virtual ~FeatureGroupingAlgorithm();

    ///Applies the algorithm. The features in the input @p maps are grouped and the output is written to the consensus map @p out
    virtual void group(const std::vector<FeatureMap > & maps, ConsensusMap & out) = 0;

    ///Applies the algorithm. The consensus features in the input @p maps are grouped and the output is written to the consensus map @p out
    /// Algorithms not supporting ConsensusMap input should simply not override this method,
    /// as the base implementation will forward the data to the FeatureMap version of group()
    virtual void group(const std::vector<ConsensusMap> & maps, ConsensusMap & out);

    /// Transfers subelements (grouped features) from input consensus maps to the result consensus map
    void transferSubelements(const std::vector<ConsensusMap> & maps, ConsensusMap & out) const;

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

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

  };

} // namespace OpenMS

#endif // OPENMS_ANALYSIS_MAPMATCHING_FEATUREGROUPINGALGORITHM_H
