FeatureDistance.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.
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// $Maintainer: Hendrik Weisser $
// $Authors: Clemens Groepl, Hendrik Weisser, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#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);
 
    ~FeatureDistance() override;
 
    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_() override;
 
    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 ignore_adduct_;
 
    bool force_constraints_;
 
    bool log_transform_;
  };
 
} // namespace OpenMS