MapAlignmentAlgorithmKD.h

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// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Johannes Veit $
// $Authors: Johannes Veit $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/QUANTITATION/KDTreeFeatureMaps.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationModelLowess.h>
 
namespace OpenMS
{
 
class OPENMS_DLLAPI MapAlignmentAlgorithmKD
{
public:
 
  MapAlignmentAlgorithmKD(Size num_maps, const Param& param);
 
  virtual ~MapAlignmentAlgorithmKD();
 
  void addRTFitData(const KDTreeFeatureMaps& kd_data);
 
  void fitLOWESS();
 
  void transform(KDTreeFeatureMaps& kd_data) const;
 
protected:
 
  virtual void updateMembers_();
 
  Size computeCCs_(const KDTreeFeatureMaps& kd_data, std::vector<Size>& cc_index) const;
 
  void getCCs_(const KDTreeFeatureMaps& kd_data, std::map<Size, std::vector<Size> >& result) const;
 
  void filterCCs_(const KDTreeFeatureMaps& kd_data, const std::map<Size, std::vector<Size> >& ccs, std::map<Size, std::vector<Size> >& filtered_ccs) const;
 
private:
 
  MapAlignmentAlgorithmKD();
 
  std::vector<TransformationModel::DataPoints> fit_data_;
 
  std::vector<TransformationModelLowess*> transformations_;
 
  Param param_;
 
  double max_pairwise_log_fc_;
 
  double rt_tol_secs_;
 
  double mz_tol_;
 
  bool mz_ppm_;
 
};
 
} // namespace OpenMS