MapAlignmentAlgorithmKD.h

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// $Maintainer: Johannes Veit $
// $Authors: Johannes Veit $
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#ifndef OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMKD_H
#define OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMKD_H

#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

#endif // OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMKD_H