FineIsotopePatternGenerator.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Hannes Rost $
// $Authors: Hannes Rost $
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#pragma once

#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopePatternGenerator.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>


namespace OpenMS
{

  class OPENMS_DLLAPI FineIsotopePatternGenerator
    : public IsotopePatternGenerator
  {

 public:

    FineIsotopePatternGenerator() = default;

    FineIsotopePatternGenerator(double stop_condition, bool absolute = false, bool use_total_prob = false) :
      stop_condition_(stop_condition),
      absolute_(absolute),
      use_total_prob_(use_total_prob)
    {}

    IsotopeDistribution run(const EmpiricalFormula&) const;

    void setThreshold(double stop_condition)
    {
      stop_condition_ = stop_condition;
    }

    double getThreshold()
    {
      return stop_condition_;
    }

    void setAbsolute(bool absolute)
    {
      absolute_ = absolute;
    }

    bool getAbsolute()
    {
      return absolute_;
    }

 protected:
    double stop_condition_ = 0.01;
    bool absolute_ = false;
    bool use_total_prob_ = false;

  };

} // namespace OpenMS