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 2002-2017.
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// $Maintainer: Hendrik Weisser $
// $Authors: Steffen Sass, Hendrik Weisser $
// --------------------------------------------------------------------------


#ifndef OPENMS_DATASTRUCTURES_QTCLUSTER_H
#define OPENMS_DATASTRUCTURES_QTCLUSTER_H

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

#include <boost/unordered_map.hpp>

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


namespace OpenMS
{
  class GridFeature;

  // Boost switch since with 1.47 several classes got moved into a new
  // boost::unordered namespace (specifically unordered_map).
  namespace OpenMSBoost
  {
#if OPENMS_BOOST_VERSION_MINOR > 47
    using namespace boost::unordered;
#else
    using namespace boost;
#endif
  }


  class OPENMS_DLLAPI QTCluster
  {
private:

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

    typedef std::pair<double, GridFeature*> NeighborPairType;
    typedef OpenMSBoost::unordered_map<Size, NeighborPairType> NeighborMap;

    GridFeature* center_point_;

    NeighborMap neighbors_;

    NeighborMapMulti* tmp_neighbors_;

    double max_distance_;

    Size num_maps_;

    double quality_;

    bool changed_;

    bool use_IDs_;

    bool valid_;

    bool collect_annotations_;

    bool finalized_;

    Int x_coord_;

    Int y_coord_;

    std::set<AASequence> annotations_;

    QTCluster();

    void computeQuality_();

    double optimizeAnnotations_();

public:

    QTCluster(GridFeature* center_point, Size num_maps,
              double max_distance, bool use_IDs, 
              Int x_coord, Int y_coord);

    virtual ~QTCluster();

    GridFeature* getCenterPoint();

    double getCenterRT() const;

    double getCenterMZ() const;

    Int getXCoord() const;

    Int getYCoord() const;

    Size size() const;

    bool operator<(QTCluster& cluster);

    void add(GridFeature* element, double distance);

    void getElements(OpenMSBoost::unordered_map<Size, GridFeature*>& elements);

    bool update(const OpenMSBoost::unordered_map<Size, GridFeature*>& removed);

    double getQuality();

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

    void setInvalid();

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

    void initializeCluster();

    void finalizeCluster();

    OpenMSBoost::unordered_map<Size, std::vector<GridFeature*> > getAllNeighbors();
  };
} // namespace OpenMS

#endif // OPENMS_DATASTRUCTURES_QTCLUSTER_H