QTClusterFinder.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    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.
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// 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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// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Steffen Sass, Hendrik Weisser $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/ANALYSIS/MAPMATCHING/BaseGroupFinder.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/COMPARISON/CLUSTERING/HashGrid.h>
#include <OpenMS/DATASTRUCTURES/GridFeature.h>
#include <OpenMS/DATASTRUCTURES/QTCluster.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureDistance.h>

#include <boost/unordered_map.hpp>

#include <list>
#include <vector>
#include <set>
#include <utility> // for pair<>

namespace OpenMS
{

  class OPENMS_DLLAPI QTClusterFinder :
    public BaseGroupFinder
  {
private:

    typedef OpenMSBoost::unordered_map< 
              std::pair<OpenMS::GridFeature*, OpenMS::GridFeature*>,
              double> PairDistances;

    typedef OpenMSBoost::unordered_map<
              OpenMS::GridFeature*, std::vector<QTCluster*> > ElementMapping;

    typedef HashGrid<OpenMS::GridFeature*> Grid;

    Size num_maps_;

    bool use_IDs_;

    double max_diff_rt_;

    double max_diff_mz_;

    int nr_partitions_;

    FeatureDistance feature_distance_;

    std::set<OpenMS::GridFeature*> already_used_;

    double getDistance_(const OpenMS::GridFeature* left, const
        OpenMS::GridFeature* right);

    void setParameters_(double max_intensity, double max_mz);

    void makeConsensusFeature_(std::list<QTCluster>& clustering,
                               ConsensusFeature& feature,
                               ElementMapping& element_mapping, Grid&);

    void computeClustering_(Grid& grid, std::list<QTCluster>& clustering);

    template <typename MapType>
    void run_(const std::vector<MapType>& input_maps, ConsensusMap& result_map);

    template <typename MapType>
    void run_internal_(const std::vector<MapType>& input_maps,
                       ConsensusMap& result_map, bool do_progress);

    void addClusterElements_(int x, int y, const Grid& grid, QTCluster& cluster,
      const OpenMS::GridFeature* center_feature);

protected:

    enum
    {
      RT = Peak2D::RT,
      MZ = Peak2D::MZ
    };

public:

    QTClusterFinder();

    ~QTClusterFinder() override;

    static const String getProductName()
    {
      return "qt";
    }

    void run(const std::vector<ConsensusMap>& input_maps,
             ConsensusMap& result_map) override;

    void run(const std::vector<FeatureMap>& input_maps,
             ConsensusMap& result_map);

    static BaseGroupFinder* create()
    {
      return new QTClusterFinder();
    }
  };
} // namespace OpenMS