// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// 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: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CHEMISTRY/ModificationsDB.h>

namespace OpenMS
{
  class OPENMS_DLLAPI CrossLinksDB :
      public ModificationsDB
  {
  public:

    /// Returns a pointer to the modifications DB (singleton)
    inline static CrossLinksDB* getInstance()
    {
      static CrossLinksDB* db_ = new CrossLinksDB;
      return db_;
    }

    /**
      @brief Adds modifications from a given file in OBO format
      
      @note readFromOBOFile should be called in a single threaded context with
      no other threads accessing the CrossLinkDB
      @throw Exception::ParseError if the file cannot be parsed correctly
    */
    void readFromOBOFile(const String& filename);

    /// Collects all modifications that can be used for identification searches
    void getAllSearchModifications(std::vector<String>& modifications) const;

  private:

      /** @name Constructors and Destructors
       */
      //@{
      /// Default constructor
      CrossLinksDB();

      /// Copy constructor
      CrossLinksDB(const CrossLinksDB& residue_db);

      /// Destructor
      ~CrossLinksDB() override;
      //@}

      /** @name Assignment
       */
      //@{
      /// Assignment operator
      CrossLinksDB & operator=(const CrossLinksDB& aa);
      //@}

  };
}

