QTCluster.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// 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
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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 <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
  {
public:
 
    // need to store more than one
    typedef std::multimap<double, const GridFeature*> NeighborList;
    typedef OpenMSBoost::unordered_map<Size, NeighborList> NeighborMapMulti;
 
    struct Neighbor
    {
      double distance;
      const GridFeature* feature;
    };
 
    typedef OpenMSBoost::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);
 
    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_;
  };
 
  // needed for the heap
  bool operator<(const QTCluster& q1, const QTCluster& q2);
} // namespace OpenMS