// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Johannes Veit $
// $Authors: Johannes Junker $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_MAPMATCHING_CONSENSUSMAPNORMALIZERALGORITHMQUANTILE_H
#define OPENMS_ANALYSIS_MAPMATCHING_CONSENSUSMAPNORMALIZERALGORITHMQUANTILE_H

#include <OpenMS/KERNEL/ConsensusMap.h>

namespace OpenMS
{

  /**
   * @brief Algorithms of ConsensusMapNormalizer
   *
   */
  class OPENMS_DLLAPI ConsensusMapNormalizerAlgorithmQuantile
  {
private:
    /// copy constructor is not implemented -> private
    ConsensusMapNormalizerAlgorithmQuantile(const ConsensusMapNormalizerAlgorithmQuantile & copyin);

    /// assignment operator is not implemented -> private
    ConsensusMapNormalizerAlgorithmQuantile & operator=(const ConsensusMapNormalizerAlgorithmQuantile & rhs);

public:
    /// default constructor is not implemented -> private
    ConsensusMapNormalizerAlgorithmQuantile();

    /// destructor is not implemented -> private
    virtual ~ConsensusMapNormalizerAlgorithmQuantile();

    /**
     * @brief normalizes the maps of the consensusMap
     * @param map ConsensusMap
     */
    static void normalizeMaps(ConsensusMap & map);

    /**
     * @brief resamples data_in and writes the results to data_out
     * @param data_in the data to be resampled
     * @param data_out the results are written to this vector
     * @param n_resampling_points the number of points to resample from data_in
     */
    static void resample(const std::vector<double> & data_in, std::vector<double> & data_out, UInt n_resampling_points);

    /**
     * @brief extracts the intensities of the features of the different maps
     * @param map ConsensusMap
     * @param out_intensities resulting data, contains the feature intensities for each map of the consensus map
     */
    static void extractIntensityVectors(const ConsensusMap & map, std::vector<std::vector<double> > & out_intensities);

    /**
     * @brief writes the intensity values in feature_ints to the corresponding features in map
     * @param feature_ints contains the new feature intensities for each map of the consensus map
     * @param map ConsensusMap the map to be updated
     */
    static void setNormalizedIntensityValues(const std::vector<std::vector<double> > & feature_ints, ConsensusMap & map);
  };

} // namespace OpenMS

#endif // OPENMS_ANALYSIS_MAPMATCHING_CONSENSUSMAPNORMALIZERALGORITHMQUANTILE_H
