// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Nikos Patikos $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/config.h>

namespace OpenMS
{
  class EmpiricalFormula;
  class IsotopeDistribution;

  /** 
      @brief Provides an interface for different isotope pattern generator methods.
      
      The IsotopePatternGenerator interface allows the developer integrate various 
      isotope pattern generator methods in the OpenMS code. It provides a run() method 
      that generates but does not hold any generated isotope distribution data in 
      the class. Instead it returns an IsotopeDistribution to the caller.

      Currently there are two implementations available:

      - CoarseIsotopePatternGenerator: a fast implementation of isotopic
        patterns that generates accurate probabilities for each isotopic peak
        but ignores the hyperfine isotopic structures (i.e. single peaks will
        be generated spaced ca. 1 Da apart, thus aggregating the peaks
        generated by 13C, 15N, 18O etc.).

      - FineIsotopePatternGenerator: an implementation for generation of fine
        resolution (high resolution) isotopic patterns containing the hyperfine
        isotopic structure. This will produce individual peaks for each element
        (i.e. the isotopic peaks of 13C, 15N, 18O etc. will all be individually
        resolved).

   */
  class OPENMS_DLLAPI IsotopePatternGenerator
  {
 public:
    IsotopePatternGenerator();
    IsotopePatternGenerator(double probability_cutoff);
    
    /** 
        @brief interface that is being used by the Isotope Pattern Generator methods.
        
        Method that calculates the isotope distribution for the given formula.

     */
    virtual IsotopeDistribution run(const EmpiricalFormula&) const = 0;
    virtual ~IsotopePatternGenerator();

 protected:
    double min_prob_;
  };
}

