KDTreeFeatureMaps.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:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    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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// $Maintainer: Johannes Veit $
// $Authors: Johannes Veit $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationModelLowess.h>
#include <OpenMS/DATASTRUCTURES/KDTree.h>
#include <OpenMS/ANALYSIS/QUANTITATION/KDTreeFeatureNode.h>
 
namespace OpenMS
{
 
class OPENMS_DLLAPI KDTreeFeatureMaps : public DefaultParamHandler
{
 
public:
 
  typedef KDTree::KDTree<2,KDTreeFeatureNode> FeatureKDTree;
 
  KDTreeFeatureMaps() :
    DefaultParamHandler("KDTreeFeatureMaps")
  {
    check_defaults_ = false;
  }
 
  template <typename MapType>
  KDTreeFeatureMaps(const std::vector<MapType>& maps, const Param& param) :
    DefaultParamHandler("KDTreeFeatureMaps")
  {
    check_defaults_ = false;
    setParameters(param);
    addMaps(maps);
  }
 
  ~KDTreeFeatureMaps() override
  {
  }
 
  template <typename MapType>
  void addMaps(const std::vector<MapType>& maps)
  {
    num_maps_ = maps.size();
 
    for (Size i = 0; i < num_maps_; ++i)
    {
      const MapType& m = maps[i];
      for (typename MapType::const_iterator it = m.begin(); it != m.end(); ++it)
      {
        addFeature(i, &(*it));
      }
    }
    optimizeTree();
  }
 
  void addFeature(Size mt_map_index, const BaseFeature* feature);
 
  const BaseFeature* feature(Size i) const;
 
  double rt(Size i) const;
 
  double mz(Size i) const;
 
  float intensity(Size i) const;
 
  Int charge(Size i) const;
 
  Size mapIndex(Size i) const;
 
  Size size() const;
 
  Size treeSize() const;
 
  Size numMaps() const;
 
  void clear();
 
  void optimizeTree();
 
  void getNeighborhood(Size index, std::vector<Size>& result_indices, double rt_tol, double mz_tol, bool mz_ppm, bool include_features_from_same_map = false, double max_pairwise_log_fc = -1.0) const;
 
  void queryRegion(double rt_low, double rt_high, double mz_low, double mz_high, std::vector<Size>& result_indices, Size ignored_map_index = std::numeric_limits<Size>::max()) const;
 
  void applyTransformations(const std::vector<TransformationModelLowess*>& trafos);
 
protected:
 
  void updateMembers_() override;
 
  std::vector<const BaseFeature*> features_;
 
  std::vector<Size> map_index_;
 
  std::vector<double> rt_;
 
  Size num_maps_;
 
  FeatureKDTree kd_tree_;
 
};
}