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 2002-2020.
//
// 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.
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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
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// 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,
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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 <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