/*-
 * SPDX-License-Identifier: BSD-2-Clause
 * 
 * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 * 
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer
 * 2. 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.
 * 
 * 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 THE COPYRIGHT OWNER OR CONTRIBUTORS 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
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/* 
	Created by: Maarten L. Hekkelman
	Date: maandag 07 januari, 2019

	Skip list for e.g. pepflip
*/

#pragma once

#include <filesystem>

#include "cif++/Structure.hpp"

struct SkipResidue
{
	std::string	asymID;
	int			seqID;
	std::string	monID;
};

typedef std::vector<SkipResidue> SkipList;

enum SkipListNumberingScheme
{
	sl_Label, sl_PDB //, sl_Auth
};

// --------------------------------------------------------------------

SkipList readSkipList(const std::filesystem::path& file,
	const mmcif::Structure& structure);

void writeSkipList(const std::filesystem::path& file,
	const mmcif::Structure& structure, const SkipList& list,
	SkipListNumberingScheme scheme = sl_Label);
