FeatureDistance.h

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// $Maintainer: Hendrik Weisser $
// $Authors: Clemens Groepl, Hendrik Weisser, Chris Bielow $
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#ifndef OPENMS_ANALYSIS_MAPMATCHING_FEATUREDISTANCE_H
#define OPENMS_ANALYSIS_MAPMATCHING_FEATUREDISTANCE_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/BaseFeature.h>

#include <limits>

namespace OpenMS
{
  class OPENMS_DLLAPI FeatureDistance :
    public DefaultParamHandler
  {
public:
    static const double infinity;

    FeatureDistance(double max_intensity = 1.0,
                    bool force_constraints = false);

    virtual ~FeatureDistance();

    FeatureDistance & operator=(const FeatureDistance & other);

    std::pair<bool, double> operator()(const BaseFeature & left,
                                       const BaseFeature & right);

protected:

    struct DistanceParams_
    {
      DistanceParams_() {}

      DistanceParams_(const String & what, const Param & global)
      {
        Param param = global.copy("distance_" + what + ":", true);
        if (what == "MZ") 
        {
          max_diff_ppm = (param.getValue("unit") == "ppm");
        }
        else
        {
          max_diff_ppm = false;
        }

        max_difference = param.getValue("max_difference");
        exponent = param.getValue("exponent");
        weight = param.getValue("weight");
        norm_factor = 1 / max_difference;

        relevant = (weight != 0.0) && (exponent != 0.0);
        if (!relevant) 
        {
            weight = 0.0;
        }
      }

      double max_difference, exponent, weight, norm_factor;
      bool max_diff_ppm, relevant;
    };

    void updateMembers_();

    inline double distance_(double diff, const DistanceParams_ & params) const;

    DistanceParams_ params_rt_, params_mz_, params_intensity_;

    double total_weight_reciprocal_;

    double max_intensity_;

    bool ignore_charge_;

    bool force_constraints_;

    bool log_transform_;
  };

} // namespace OpenMS

#endif  // OPENMS_ANALYSIS_MAPMATCHING_FEATUREDISTANCE_H