/* 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 CROSS_LINKER_HPP
#define CROSS_LINKER_HPP
//#warning "Entering CROSS_LINKER_HPP"


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


namespace msXpSmassXpert
{

class CrossLinker : public PolChemDefEntity,
                    public msXpSlibmass::Formula,
                    public msXpSlibmass::Ponderable
{
  protected:
  // We do not own the modifications below, the pointers refer to
  // modifications in the polymer chemistry definition.
  QList<Modif *> m_modifList;

  public:
  CrossLinker(const PolChemDef *, const QString &, const QString &);

  CrossLinker(const CrossLinker &);

  ~CrossLinker();

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

  bool setModifAt(Modif *, int);
  bool appendModif(Modif *);
  const Modif *modifAt(int) const;
  bool removeModifAt(int);

  QString formula() const;

  QList<Modif *> &modifList();

  int hasModif(const QString &);

  virtual bool operator==(const CrossLinker &) const;

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

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

  bool calculateMasses();

  bool renderXmlClkElement(const QDomElement &, int);
  bool renderXmlClkElement(const QDomElement &);
  bool renderXmlClkElementV3(const QDomElement &);

  QString *formatXmlClkElement(int, const QString & = QString("  "));
};

} // namespace msXpSmassXpert


#endif // CROSS_LINKER_HPP
