// --------------------------------------------------------------------------
//                   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
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/METADATA/ID/ScoredProcessingResult.h>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>

#include <boost/multi_index_container.hpp>
#include <boost/multi_index/ordered_index.hpp>
#include <boost/multi_index/member.hpp>

namespace OpenMS
{
  namespace IdentificationDataInternal
  {
    struct IdentifiedCompound: public ScoredProcessingResult
    {
      String identifier;

      EmpiricalFormula formula;

      String name;

      String smile;

      String inchi;

      explicit IdentifiedCompound(
        const String& identifier,
        const EmpiricalFormula& formula = EmpiricalFormula(),
        const String& name = "", const String& smile = "",
        const String& inchi = "", const AppliedProcessingSteps&
        steps_and_scores = AppliedProcessingSteps()):
        ScoredProcessingResult(steps_and_scores), identifier(identifier),
        formula(formula), name(name), smile(smile), inchi(inchi)
      {
      }

      IdentifiedCompound(const IdentifiedCompound& other) = default;
    };

    // identified compounds indexed by their identifiers:
    typedef boost::multi_index_container<
      IdentifiedCompound,
      boost::multi_index::indexed_by<
        boost::multi_index::ordered_unique<boost::multi_index::member<
          IdentifiedCompound, String, &IdentifiedCompound::identifier>>>
      > IdentifiedCompounds;
    typedef IteratorWrapper<IdentifiedCompounds::iterator> IdentifiedCompoundRef;
  }
}
