/* 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_LINK_HPP
#define CROSS_LINK_HPP
//#warning "Entering CROSS_LINK_HPP"


/////////////////////// Local includes
#include <massxpert/nongui/CrossLinker.hpp>
#include <massxpert/nongui/Monomer.hpp>

namespace msXpSmassXpert
{

class Polymer;


enum CrossLinkEncompassed
{
  CROSS_LINK_ENCOMPASSED_NO      = 0,
  CROSS_LINK_ENCOMPASSED_PARTIAL = 1,
  CROSS_LINK_ENCOMPASSED_FULL    = 2,
};

class CrossLink : public CrossLinker
{
  protected:
  // We do not own these two monomers and polymer.
  QPointer<Polymer> mp_polymer;
  QList<const Monomer *> m_monomerList;

  QString m_comment;

  public:
  CrossLink(const PolChemDef *,
            Polymer *,
            const QString &,
            const QString &,
            const QString & = QString());

  CrossLink(const CrossLink &);

  CrossLink(const CrossLinker &, Polymer *, const QString & = QString());

  ~CrossLink();

  bool setMonomerAt(Monomer *, int);
  bool appendMonomer(const Monomer *);
  const Monomer *monomerAt(int);
  bool removeMonomerAt(int);

  void setPolymer(Polymer *);
  Polymer *polymer();

  void setComment(const QString &);
  const QString &comment() const;

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

  int populateMonomerList(QString);
  QList<const Monomer *> *monomerList();
  int monomerIndexList(QList<int> *);
  QString monomerIndexText();
  QString monomerPosText();

  int involvesMonomer(const Monomer *) const;
  const Monomer *firstMonomer() const;
  int encompassedBy(int, int, int *in = 0, int * = 0);
  int encompassedBy(const CoordinateList &, int *in = 0, int * = 0);

  int involvedMonomers(QList<Monomer *> *);


  bool validate();

  virtual bool calculateMasses();

  virtual bool accountMasses(double * = 0, double * = 0, int = 1);
  virtual bool accountMasses(Ponderable *, int = 1);

  QString *prepareResultsTxtString();
};

} // namespace msXpSmassXpert


#endif // CROSS_LINK_HPP
