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 2002-2020.
//
// 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
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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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 <boost/heap/fibonacci_heap.hpp>
 
#include <list>
#include <vector>
#include <unordered_set>
#include <utility> // for pair<>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI QTClusterFinder :
    public BaseGroupFinder
  {
  public:
 
    typedef OpenMSBoost::unordered_map< 
              std::pair<OpenMS::GridFeature*, OpenMS::GridFeature*>,
              double> PairDistances;
 
    typedef OpenMSBoost::unordered_map<
              const OpenMS::GridFeature*, std::unordered_set<Size> > ElementMapping;
 
    typedef boost::heap::fibonacci_heap<QTCluster> Heap;
 
    typedef HashGrid<OpenMS::GridFeature*> Grid;
 
  private:
    Size num_maps_;
 
    bool use_IDs_;
 
    double max_diff_rt_;
 
    double max_diff_mz_;
 
    int nr_partitions_;
 
    FeatureDistance feature_distance_;
 
    std::unordered_set<const OpenMS::GridFeature*> already_used_;
 
    double getDistance_(const OpenMS::GridFeature* left, const
        OpenMS::GridFeature* right);
 
    void setParameters_(double max_intensity, double max_mz);
 
    bool makeConsensusFeature_(Heap& cluster_heads,
                               ConsensusFeature& feature,
                               ElementMapping& element_mapping,
                               const Grid& grid,
                               const std::vector<Heap::handle_type>& handles);
 
    void computeClustering_(const Grid& grid,
                            Heap& cluster_heads,
                            std::vector<QTCluster::BulkData>& cluster_data,
                            std::vector<Heap::handle_type>& handles,
                            ElementMapping& element_mapping);
 
    void removeFromElementMapping_(const QTCluster& cluster,
                                   ElementMapping& element_mapping);
    
    void createConsensusFeature_(ConsensusFeature& feature, const double quality, 
                                 const QTCluster::Elements& elements);
 
    void updateClustering_(ElementMapping& element_mapping,
                           const Grid& grid, 
                           const QTCluster::Elements& elements,
                           Heap& cluster_heads,
                           const std::vector<Heap::handle_type>& handles,
                           Size best_id);
 
    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_(const Grid& grid, QTCluster& cluster);
 
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