QTCluster.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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//    may be used to endorse or promote products derived from this software
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// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Steffen Sass, Hendrik Weisser $
// --------------------------------------------------------------------------


#pragma once

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/OpenMSConfig.h>
#include <OpenMS/config.h>

#include <unordered_map>

#include <map> // for multimap<>
#include <vector> // for vector<>
#include <set> // for set<>
#include <utility> // for pair<>

namespace OpenMS
{
  class GridFeature;

  class OPENMS_DLLAPI QTCluster
  {
public:

    // need to store more than one
    typedef std::multimap<double, const GridFeature*> NeighborList;
    typedef std::unordered_map<Size, NeighborList> NeighborMapMulti;

    struct Neighbor
    {
      double distance;
      const GridFeature* feature;
    };

    typedef std::unordered_map<Size, Neighbor> NeighborMap;

    struct Element
    {
      Size map_index;
      const GridFeature* feature;
    };

    typedef std::vector<Element> Elements;

    class OPENMS_DLLAPI BulkData
    {
      friend class QTCluster;

      public:

        BulkData(const OpenMS::GridFeature* const center_point, 
                Size num_maps, double max_distance,
                Int x_coord, Int y_coord, Size id);
      
      private:

        const GridFeature* const center_point_;

        Size id_;

        NeighborMap neighbors_;

        NeighborMapMulti tmp_neighbors_;

        double max_distance_;

        Size num_maps_;

        Int x_coord_;

        Int y_coord_;

        std::set<AASequence> annotations_;
    };

    QTCluster(BulkData* const data, bool use_IDs);

    QTCluster() = delete;

    QTCluster(const QTCluster& rhs) = default;

    QTCluster& operator=(const QTCluster& rhs) = default;

    QTCluster(QTCluster&& rhs) = default;

    QTCluster& operator=(QTCluster&& rhs) = default;

    ~QTCluster() = default;

    const GridFeature* getCenterPoint() const;

    Size getId() const;

    double getCenterRT() const;

    double getCenterMZ() const;

    Int getXCoord() const;

    Int getYCoord() const;

    Size size() const;

    bool operator<(const QTCluster& cluster) const;

    void add(const GridFeature* const element, double distance);

    Elements getElements() const;

    bool update(const Elements& removed);

    double getQuality();

    double getCurrentQuality() const;

    const std::set<AASequence>& getAnnotations();

    void setInvalid();

    inline bool isInvalid() const
    {
      return !valid_;
    }

    void initializeCluster();

    void finalizeCluster();

    Elements getAllNeighbors() const;

    private:
      void computeQuality_();

      double optimizeAnnotations_();

      void makeSeqTable_(std::map<AASequence, std::map<Size,double>>& seq_table) const;
      
      void recomputeNeighbors_();

      double quality_;

      BulkData* data_;

      bool valid_;

      bool changed_;

      bool use_IDs_;

      bool collect_annotations_;

      bool finalized_;
  };

} // namespace OpenMS