/* 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 CLEAVE_MOTIF_HPP
#define CLEAVE_MOTIF_HPP


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


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


namespace msXpSmassXpert
{

//! The CleaveMotif class provides cleavage motifs.
/*! When a polymer sequence cleavage occurs, using for example the
  specification "Lys/;Arg/;-Lys/Pro", a number of actions need be
  performed prior to listing the oligomers obtained following
  cleavage.

  The "Lys/;Arg/;-Lys/Pro" specification gets crunched in a number of
  steps and motifs are generated for it. In this specific case we'll
  have three motifs with the following data:

  - First motif:
  - "Lys/"
  - code list [0] = "Lys"
  - offset = 1('/' indicates that cut is right of monomer)
  - is for cleavage ? = true

  - Second motif:
  - "Arg/"
  - code list [0] = "Arg"
  - offset = 1('/' indicates that cut is right of monomer)
  - is for cleavage ? = true

  - Third motif:
  - "-Lys/Pro"
  - code list [0] = "Lys", [1] = "Pro"
  - offset = 1('/' indicates that cut is right of monomer)
  - is for cleavage ? = false

  Thanks to this deconstruction(from "Lys/;Arg/;-Lys/Pro" to the 3
  motifs above) is the polymer sequence cleaved according to the
  specification.
*/
class CleaveMotif : public PolChemDefEntity
{
  private:
  //! Motif.
  QString m_motif;

  //! List of codes in motif.
  QStringList m_codeList;

  //! Offset of the cleavage.
  int m_offset;

  //! Tells if motif is for cleavage.
  bool m_isForCleave;

  public:
  CleaveMotif(const PolChemDef *,
              QString,
              const QString & = QString(),
              int             = 0,
              bool            = false);

  CleaveMotif(const CleaveMotif &);


  ~CleaveMotif();

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

  CleaveMotif &operator=(const CleaveMotif &);

  void setMotif(const QString &);
  const QString &motif();

  const QStringList &codeList() const;

  void setOffset(int);
  int offset();

  void setForCleave(bool);
  bool isForCleave();

  int parse(const QString &);

#pragma clang diagnostic push
#pragma clang diagnostic ignored "-Woverloaded-virtual"
  bool validate();
#pragma clang diagnostic pop
};

} // namespace msXpSmassXpert


#endif // CLEAVE_MOTIF_HPP
