/******************************************************************************
**
** Copyright (C) 2009-2011 Kyle Lutz <kyle.r.lutz@gmail.com>
** All rights reserved.
**
** This file is a part of the chemkit project. For more information
** see <http://www.chemkit.org>.
**
** Redistribution and use in source and binary forms, with or without
** modification, are permitted provided that the following conditions
** are met:
**
**   * 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 the chemkit project nor the names of its
**     contributors may be used to endorse or promote products derived
**     from this software without specific prior written permission.
**
** 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,
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** LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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******************************************************************************/

#ifndef CHEMKIT_POLYMERCHAIN_H
#define CHEMKIT_POLYMERCHAIN_H

#include "chemkit.h"

#include <string>
#include <vector>

namespace chemkit {

class Polymer;
class Residue;
class PolymerChainPrivate;

class CHEMKIT_EXPORT PolymerChain
{
public:
    // properties
    void setName(const std::string &name);
    std::string name() const;
    size_t size() const;
    bool isEmpty() const;
    Polymer* polymer() const;

    // structure
    void addResidue(Residue *residue);
    void appendResidue(Residue *residue);
    void prependResidue(Residue *residue);
    void insertResidue(size_t index, Residue *residue);
    bool removeResidue(Residue *residue);
    bool takeResidue(Residue *residue);
    Residue* residue(size_t index) const;
    std::vector<Residue *> residues() const;
    size_t residueCount() const;
    int indexOf(const Residue *residue) const;
    std::string sequenceString() const;
    int sequenceNumber(const Residue *residue) const;

private:
    // construction and destruction
    PolymerChain(Polymer *polymer);
    ~PolymerChain();

    CHEMKIT_DISABLE_COPY(PolymerChain)

    friend class Polymer;

private:
    PolymerChainPrivate* const d;
};

} // end chemkit namespace

#endif // CHEMKIT_POLYMERCHAIN_H
