/* massXpert - the true massist's program.
   --------------------------------------
   Copyright(C) 2006,2007 Filippo Rusconi

   http://www.massxpert.org/massXpert

   This file is part of the massXpert project.

   The massxpert project is the successor to the "GNU polyxmass"
   project that is an official GNU project package(see
   www.gnu.org). The massXpert project is not endorsed by the GNU
   project, although it is released ---in its entirety--- under the
   GNU General Public License. A huge part of the code in massXpert
   is actually a C++ rewrite of code in GNU polyxmass. As such
   massXpert was started at the Centre National de la Recherche
   Scientifique(FRANCE), that granted me the formal authorization to
   publish it under this Free Software License.

   This software is free software; you can redistribute it and/or
   modify it under the terms of the GNU  General Public
   License version 3, as published by the Free Software Foundation.
   

   This software 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 software; if not, write to the

   Free Software Foundation, Inc.,

   51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
*/


/////////////////////// Local includes
#include "cleaveMotif.hpp"
#include "polymer.hpp"


namespace massXpert
{

  //! Constructs a cleavage motif.
  /*! 
  
    \param polChemDef Polymer chemistry definition. Cannot be 0.

    \param name Name. Cannot be empty.

    \param str Motif in the form of "Lys/;Arg/;-Lys/Pro".

    \param offset Offset of the cleavage.

    \param isForCleave Tells if motif is for cleavage.
  */
  CleaveMotif::CleaveMotif(const PolChemDef *polChemDef, 
			    QString name, const QString &str, 
			    int offset, bool isForCleave)
    : PolChemDefEntity(polChemDef, name), 
      m_motif(str), m_offset(offset), m_isForCleave(isForCleave)
  {
  }


  //! Constructs a copy of \p other.
  /*!

    \param other cleavage motif to be used as a mold.
  */
  CleaveMotif::CleaveMotif(const CleaveMotif &other)
    : PolChemDefEntity(other),
      m_motif(other.m_motif), m_codeList(other.m_codeList),
      m_offset(other.m_offset), m_isForCleave(other.m_isForCleave)
  {
  }

  //! Destroys the cleavage motif.
  CleaveMotif::~CleaveMotif()
  {
  }


  //! Modifies \p other to be identical to \p this.
  /*!  \param other cleavage motif.
   */
  void 
  CleaveMotif::clone(CleaveMotif *other) const
  {
    Q_ASSERT(other);

    PolChemDefEntity::clone(other);

    other->m_motif = m_motif;

    other->m_codeList.clear();
    other->m_codeList = m_codeList;
  
    other->m_offset = m_offset;
    other->m_isForCleave = m_isForCleave;
  }


  //! Modifies \p this  to be identical to \p other.
  /*!  \param other cleavage motif to be used as a mold.
   */
  void
  CleaveMotif::mold(const CleaveMotif &other)
  {
    if (&other == this)
      return;

    PolChemDefEntity::mold(other);

    m_motif = other.m_motif;
    m_codeList = other.m_codeList;
    m_offset = other.m_offset;
    m_isForCleave = other.m_isForCleave;
  }


  //! Assigns other to \p this cleavage motif.
  /*! \param other cleavage motif used as the mold to set values to \p
    this instance.
  
    \return a reference to \p this cleavage motif.
  */
  CleaveMotif &
  CleaveMotif::operator =(const CleaveMotif &other)
  {
    if (&other != this)
      mold(other);
  
    return *this;
  }


  //! Sets the motif.
  /*!  \param str new motif.
   */
  void 
  CleaveMotif::setMotif(const QString &str)
  {
    m_motif = str;
  }


  //! Returns the motif.
  /*!  
    \return the motif.
  */
  const QString &
  CleaveMotif::motif()
  {
    return m_motif;
  }



  //! Returns the string list of codes in the motif.
  /*!  
    \return the string list of codes in the motif.
  */
  const QStringList &
  CleaveMotif::codeList() const
  {
    return m_codeList;
  }



  //! Sets the offset.
  /*!  \param value new offset.
   */
  void 
  CleaveMotif::setOffset(int value)
  {
    m_offset = value;
  }


  //! Returns the offset.
  /*!  
    \return the offset.
  */
  int 
  CleaveMotif::offset()
  {
    return m_offset;
  }


  //! Sets if motif is for cleavage.
  /*!  \param value if motif is for cleavage.
   */
  void 
  CleaveMotif::setForCleave(bool value)
  {
    m_isForCleave = value;
  }


  //! Returns if motif is for cleavage.
  /*!  \return if motif is for cleavage.
   */
  bool 
  CleaveMotif::isForCleave()
  {
    return m_isForCleave;
  }


  //! Parses a cleavage site.
  /*! Upon parsing of a cleavage site, this cleavage motif is filled
    with data.
  
    \param site Cleavage site in the form "Lys/Pro" or "KKGK/RRGK".

    \return the number of monomer codes in the motif, -1 upon error.
  */
  int
  CleaveMotif::parse(const QString &site)
  {
    const QList<Monomer *> &refList = mp_polChemDef->monomerList();
  
    QString code;
    QString error;
    QString local = site;
  
    int index = 0;
    int count = 0;
  
    // We get something like "Lys/Pro" or something like "KKGK/RRGK" and
    // we have to make three things: 
    //
    // 1. change the site "KKGK/RRGK" to a motif string(KKGKRRGK).
    //
    // 2. set the offset member to the index of '/' in the initial site
    // string.  
    //
    // 3. make an array of codes with the motif.
  
    Sequence sequence(local);
  
    while(1)
      {
	code.clear();
      
	if(sequence.nextCode(&code, &index, &error, 
			       mp_polChemDef->codeLength()) == -1)
	  {
	    if (error == "/")
	      {
		m_offset = count;
	      
		// qDebug() << __FILE__ << __LINE__
		// << "Found / at code position" << m_offset;
	      
		// Increment index so that we iterate in the next code
		// at next round.
		++index;

		continue;
	      }
	  	      
	    // There was an error parsing the site sequence. If the err
	    // string contains a space, that is not serious, we could
	    // skip that.
	  
	    qDebug() << __FILE__ << __LINE__
		      << "Failed to parse cleavage site"
		      << site.toAscii();
	  
	    return -1;
	  }
      
	// There might have been no error, but that does not means that
	// we necessarily got a code.
	if(code.isEmpty())
	  {
	    // We arrived at the end of a code parsing step(either
	    // because the current 'local' cleavage site(that is
	    // 'sequence') was finished parsing or because we finished
	    // parsing one of its monomer codes.
	    break;
	  }
      
	// At this point we actually had a code.
      
	//       qDebug() << __FILE__ << __LINE__
	// 		<< "Got next code:" << code.toAscii();
      
	// At this point, 'code' contains something that looks like a
	// valid code, but we still have to make sure that this code
	// actually is in our list of monomer codes...

	if(Monomer::isCodeInList(code, refList) == -1)
	  {
	    qDebug() << __FILE__ << __LINE__
		      << "Monomer code" << code
		      << " is not in the monomer list.";
	  
	    return -1;
	  }
      
	// At the end m_motif will contain KKGKRRGK, while site was
	// "KKGK/RRGK" KKGKRRGK
	m_motif += code;
      
	// Add the newly parsed code to the code list.
	m_codeList << code;
      
	++count;
      
	// Increment index so that we iterate in the next code at next
	// round.
	++index;
      }
  
    // Return the number of successfully parsed monomer codes for the
    // 'site' string.
    Q_ASSERT(count == m_codeList.size());
  
    return count;
  }


  bool
  CleaveMotif::validate()
  {
    Q_ASSERT(0);
    return true;
  }

} // namespace massXpert