// --------------------------------------------------------------------------
//                   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,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
//

#pragma once

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>

#include <string>

#define OPENMS_CHEMISTRY_ELEMENT_NAME_DEFAULT "unknown"
#define OPENMS_CHEMISTRY_ELEMENT_SYMBOL_DEFAULT "??"
#define OPENMS_CHEMISTRY_ELEMENT_WEIGHT_DEFAULT 0.0
#define OPENMS_CHEMISTRY_ELEMENT_ATOMICNUMBER_DEFAULT 0

namespace OpenMS
{
  /** @ingroup Chemistry

      @brief Representation of an element

      This contains information on an element and its isotopes, including a
      common name, atomic symbol and mass/abundance of its isotopes.
  */
  class OPENMS_DLLAPI Element
  {
public:

   
    /** @name Constructor and Destructors
    */
    //@{
    /// default constructor
    Element();

    /// copy constructor
    Element(const Element & element);

    /// detailed constructor
    Element(const std::string & name,
            const std::string & symbol,
            unsigned int atomic_number,
            double average_weight,
            double mono_weight,
            const IsotopeDistribution & isotopes);

    /// destructor
    virtual ~Element();
    //@}

    /** @name Accessors
    */
    //@{
    /// sets unique atomic number
    void setAtomicNumber(unsigned int atomic_number);

    /// returns the unique atomic number
    unsigned int getAtomicNumber() const;

    /// sets the average weight of the element
    void setAverageWeight(double weight);

    /// returns the average weight of the element
    double getAverageWeight() const;

    /// sets the mono isotopic weight of the element
    void setMonoWeight(double weight);

    /// returns the mono isotopic weight of the element
    double getMonoWeight() const;

    /// sets the isotope distribution of the element
    void setIsotopeDistribution(const IsotopeDistribution & isotopes);

    /// returns the isotope distribution of the element
    const IsotopeDistribution & getIsotopeDistribution() const;

    /// set the name of the element
    void setName(const std::string & name);

    /// returns the name of the element
    const std::string & getName() const;

    /// sets symbol of the element
    void setSymbol(const std::string & symbol);

    /// returns symbol of the element
    const std::string & getSymbol() const;
    //@}

    /** @name Assignment
    */
    //@{
    /// assignment operator
    Element & operator=(const Element & element);
    //@}

    /** @name Predicates
    */
    //@{
    /// equality operator
    bool operator==(const Element & element) const;

    /// inequality operator
    bool operator!=(const Element & element) const;

    /// less operator
    bool operator<(const Element & element) const;
    //@}

    /// writes the element to an output stream
    friend OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const Element & element);

protected:

    /// name of the element
    std::string name_;

    /// symbol of the element
    std::string symbol_;

    /// atomic number of the element
    unsigned int atomic_number_;

    /// average weight over all isotopes
    double average_weight_;

    /// mono isotopic weight of the most frequent isotope
    double mono_weight_;

    /// distribution of the isotopes (mass and natural frequency)
    IsotopeDistribution isotopes_;
  };

  OPENMS_DLLAPI std::ostream & operator<<(std::ostream &, const Element &);

} // namespace OpenMS

