/* BEGIN software license
 *
 * msXpertSuite - mass spectrometry software suite
 * -----------------------------------------------
 * Copyright(C) 2009,...,2018 Filippo Rusconi
 *
 * http://www.msxpertsuite.org
 *
 * This file is part of the msXpertSuite project.
 *
 * The msXpertSuite project is the successor of the massXpert project. This
 * project now includes various independent modules:
 *
 * - massXpert, model polymer chemistries and simulate mass spectrometric data;
 * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program. If not, see <http://www.gnu.org/licenses/>.
 *
 * END software license
 */


#ifndef MONOMER_HPP
#define MONOMER_HPP
//#warning "Entering MONOMER_HPP"


/////////////////////// Qt includes
#include <QString>


/////////////////////// Local includes
#include <massxpert/nongui/PolChemDefEntity.hpp>
#include <libmass/Formula.hpp>
#include <libmass/Ponderable.hpp>
#include <massxpert/nongui/PropListHolder.hpp>
#include <massxpert/nongui/CalcOptions.hpp>
#include <massxpert/nongui/Modif.hpp>


namespace msXpSmassXpert
{

//! The Monomer class provides a monomer.

/*! A monomer is the building block of a polymer sequence. It is
  mainly characterized by a name, a code and a formula.
 */
class Monomer : public PolChemDefEntity,
                public msXpSlibmass::Formula,
                public msXpSlibmass::Ponderable,
                public PropListHolder
{
  private:
  //! Code.
  QString m_code;

  QList<Modif *> *mpa_modifList;

  public:
  Monomer(const PolChemDef *,
          QString,
          QString = QString(),
          QString = QString());

  ~Monomer();

  Monomer *clone() const;

#pragma clang diagnostic push
#pragma clang diagnostic ignored "-Woverloaded-virtual"
  void clone(Monomer *) const;
  void mold(const Monomer &);
#pragma clang diagnostic pop

  void setCode(const QString &);
  QString code() const;

  bool operator==(const Monomer &) const;
  bool operator!=(const Monomer &) const;

  bool checkCodeSyntax() const;

  int isCodeKnown() const;
  static int
  isCodeInList(const QString &, const QList<Monomer *> &, Monomer * = 0);

  int isNameKnown() const;
  static int
  isNameInList(const QString &, const QList<Monomer *> &, Monomer * = 0);

  QString formula() const;

  QList<Modif *> *modifList() const;

  bool isModifTarget(const Modif &) const;
  bool modify(Modif *, bool, QStringList &);
  bool unmodify();
  bool unmodify(Modif *);
  bool isModified() const;

  int modifCount(const QString &);

#pragma clang diagnostic push
#pragma clang diagnostic ignored "-Woverloaded-virtual"
  bool validate();
  bool calculateMasses(int = MONOMER_CHEMENT_NONE);
  bool accountMasses(double * = 0, double * = 0, int = 1) const;
  bool accountMasses(Ponderable *, int) const;
#pragma clang diagnostic pop

  bool renderXmlMnmElement(const QDomElement &, int);

  QString *formatXmlMnmElement(int, const QString & = QString("  "));

  bool renderXmlMonomerElement(const QDomElement &, int);
  bool renderXmlMonomerElementV2(const QDomElement &, int);

  QString *formatXmlMonomerElement(int, const QString & = QString("  ")) const;

  void debugPutStdErr() const;
};

} // namespace msXpSmassXpert


#endif // MONOMER_HPP
