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 2002-2018.
//
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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_;

};
}