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fragRule.cpp

/* 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 "fragRule.hpp"
#include "polChemDef.hpp"


namespace massXpert
{

  //! Constructs a fragmentation rule.
  /*! 
  
    \param polChemDef Polymer chemistry definition. Cannot be 0.

    \param name Name. Cannot be empty.

    \param prevCode Previous monomer code. Defaults to the null string.

    \param currCode  Current monomer code. Defaults to the null string.

    \param nextCode Next monomer code. Defaults to the null string.

    \param formula Formula. Defaults to the null string.

    \param comment Comment. Defaults to the null string.
  */
00063   FragRule::FragRule(const PolChemDef *polChemDef, QString name, 
                  QString prevCode,
                  QString currCode, 
                  QString nextCode,
                  QString formula,
                  const QString &comment)
    : PolChemDefEntity(polChemDef, name), Formula(formula),
      m_prevCode(prevCode), m_currCode(currCode), m_nextCode(nextCode),
      m_comment(comment)
  {
  }


  //! Constructs a copy of \p other.
  /*!  \param other fragmentation rule to be used as a mold.
   */
00079   FragRule::FragRule(const FragRule &other)
    : PolChemDefEntity(other), Formula(other), 
      m_prevCode(other.m_prevCode), 
      m_currCode(other.m_currCode), 
      m_nextCode(other.m_nextCode),
      m_comment(other.m_comment)
  {
  }


  //! Destroys the fragmentation rule.
00090   FragRule::~FragRule()
  {
  }

  
  //! Creates a new fragmentation rule initialized according to \c this.
  /*!  \return The newly created fragmentation rule, which must be
    deleted when no longer in use.
  */
  FragRule * 
00100   FragRule::clone() const
  {
    FragRule *other = new FragRule(*this);
  
    return other;
  }


  //! Modifies \p other to be identical to \p this.
  /*!  \param other fragmentation rule.
   */
  void
00112   FragRule::clone(FragRule *other) const
  {
    Q_ASSERT(other);

    if (other == this)
      return;
  
    PolChemDefEntity::clone(other);
    Formula::clone(other);

    other->m_prevCode = m_prevCode;
    other->m_currCode = m_currCode;
    other->m_nextCode = m_nextCode;
    other->m_comment = m_comment;
  }


  //! Modifies \p this  to be identical to \p other.
  /*!  \param other fragmentation rule to be used as a mold.
   */
  void 
00133   FragRule::mold(const FragRule &other)
  {
    if (&other == this)
      return;
  
    PolChemDefEntity::mold(other);
    Formula::mold(other);

    m_prevCode = other.m_prevCode;
    m_currCode = other.m_currCode;
    m_nextCode = other.m_nextCode;
    m_comment = other.m_comment;
  }


  //! Assigns other to \p this fragmentation rule.
  /*! \param other fragmentation rule used as the mold to set values to \p this
    instance.
  
    \return a reference to \p this fragmentation rule.
  */
  FragRule & 
00155   FragRule::operator =(const FragRule &other)
  {
    if (&other != this)
      mold(other);
  
    return *this;
  }


  //! Sets the previous monomer code.
  /*! \param str new code.
   */
  void 
00168   FragRule::setPrevCode(const QString &str)
  {
    m_prevCode = str;
  }


  //! Returns the previous monomer code.
  /*! \return the code.
   */
  QString
00178   FragRule::prevCode() const
  {
    return m_prevCode;
  }


  //! Sets the current monomer code.
  /*! \param str new code.
   */
  void 
00188   FragRule::setCurrCode(const QString &str)
  {
    m_currCode = str;
  }


  //! Returns the current monomer code.
  /*! \return the code.
   */
  QString
00198   FragRule::currCode() const
  {
    return m_currCode;
  }


  //! Sets the next monomer code.
  /*! \param str new code.
   */
  void 
00208   FragRule::setNextCode(const QString &str)
  {
    m_nextCode = str;
  }


  //! Returns the next monomer code.
  /*! \return the code.
   */
  QString
00218   FragRule::nextCode() const
  {
    return m_nextCode;
  }


  //! Sets the comment.
  /*! \param str new comment.
   */
  void 
00228   FragRule::setComment(const QString &str)
  {
    m_comment = str;
  }


  //! Returns the comment.
  /*! \return the comment.
   */
  QString
00238   FragRule::comment() const
  {
    return m_comment;
  }


  //! Searches a fragmentation rule in a list.
  /*! Searches for a fragmentation rule having a name identical to
    argument \p str in \p refList. If such fragmentation rule is found,
    and if \p other is non-0, the found fragmentation rule's data are
    copied into \p other.
  
    \param str name.

    \param refList list of fragmentation rules.
  
    \param other fragmentation rule to be updated with data in the found
    fragmentation rule.  Defaults to 0, in which case no update occurs.
  
    \return the int index of the found fragmentation rule or -1 if none
    is found or if \p str is empty.
  */
  int 
00261   FragRule::isNameInList(const QString &str, 
                    const QList<FragRule*> &refList,
                    FragRule *other)
  {
    FragRule *fragRule = 0;
  
    if (str.isEmpty())
      return -1;
  
    for (int iter = 0; iter < refList.size(); ++iter)
      {
      fragRule = refList.at(iter);
      Q_ASSERT(fragRule);
      
      if(fragRule->m_name == str)
        {
          if (other)
            fragRule->clone(other);
        
          return iter;
        }
      }
  
    return -1;
  }


  //! Validates the fragmentation rule.
  /*! 
    \return true upon success, false otherwise.
  */
  bool 
00293   FragRule::validate()
  {
    const QList<Monomer *> &monomerRefList = mp_polChemDef->monomerList();
    const QList<Atom *> &atomRefList = mp_polChemDef->atomList();
  
    if (m_name.isEmpty())
      return false;
  
    if (!m_prevCode.isEmpty())
      if (Monomer::isCodeInList(m_prevCode, monomerRefList) == -1)
      return false;
  
    if (!m_currCode.isEmpty())
      if (Monomer::isCodeInList(m_currCode, monomerRefList) == -1)
      return false;
  
    if (!m_nextCode.isEmpty())
      if (Monomer::isCodeInList(m_nextCode, monomerRefList) == -1)
      return false;
  
    return Formula::validate(atomRefList);
  
    return true;
  }



  //! Parses a fragmentation rule XML element.
  /*! Parses the fragmentation specification XML element passed as
    argument and sets its data to \p this fragmentation rule(this is
    called XML rendering).
  
    \param element XML element to be parsed and rendered.
  
    \return true if parsing and formula validation were successful,
    false otherwise.

    \sa formatXmlFgrElement(int offset, const QString &indent).
  */
  bool 
00333   FragRule::renderXmlFgrElement(const QDomElement &element)
  {
    QDomElement child;

    bool prevSet = false;
    bool currSet = false;
    bool nextSet = false;
    bool commentSet = false;

    /* The xml node we are in is structured this way:
     *
     * <fgr>
     *   <name>one_rule</name>
     *   <formula>+H2O</formula>
     *   <prev-mnm-code>M</prev-mnm-code>
     *   <this-mnm-code>Y</this-mnm-code>
     *   <next-mnm-code>T</next-mnm-code>
     *   <comment>opt_comment</comment>
     * </fgr>
     *   
     * And the element parameter points to the 
     *
     * <fgr> element tag:
     *  ^
     *  |
     *  +----- here we are right now.
     * 
     * Which means that element.tagName() == "fgr" and that
     * we'll have to go one step down to the first child of the 
     * current node in order to get to the <name> element.
     *
     * The DTD: 
     *    <!ELEMENT fgr(name,formula,prev-mnm-code?,
     *                   this-mnm-code?,next-mnm-code?,comment?)>
     */

    if (element.tagName() != "fgr")
      return false;
  
    child = element.firstChildElement();
  
    if (child.isNull() || child.tagName() != "name")
      return false;
  
    m_name = child.text();

    child = child.nextSiblingElement();

    if (child.isNull() || child.tagName() != "formula")
      return false;

    if (!Formula::renderXmlFormulaElement(child))
      return false;
  
    // Since the following items are not obligatory, we have to while()
    // until we have no more items...
  
    child = child.nextSiblingElement();
  
    while(! child.isNull())
      {
      if(child.tagName() == "prev-mnm-code")
        {
          if (prevSet)
            return false;
          else
            {
            m_prevCode = child.text();
            prevSet = true;
            }
        }
      else if (child.tagName() == "curr-mnm-code")
        {
          if (currSet)
            return false;
          else
            {
            m_currCode = child.text();
            currSet = true;
            }
        }
      else if (child.tagName() == "next-mnm-code")
        {
          if (nextSet)
            return false;
          else
            {
            m_nextCode = child.text();
            nextSet = true;
            }
        }
      else if (child.tagName() == "comment")
        {
          if (commentSet)
            return false;
          else
            {
            m_comment = child.text();
            commentSet = true;
            }
        }
      
      child = child.nextSiblingElement();
      }

    if (!validate())
      return false;

    return true;
  }


  //! Formats a string suitable to use as an XML element.
  /*! Formats a string suitable to be used as an XML element in a
    polymer chemistry definition file. The typical fragmentation
    rule element that is generated in this function looks like
    this:

    \verbatim 
    <fgr>
    <name>a-fgr-2</name>
    <formula>+H100</formula>
    <prev-mnm-code>F</prev-mnm-code>
    <curr-mnm-code>D</curr-mnm-code>
    <next-mnm-code>E</next-mnm-code>
    <comment>comment here!</comment>
    </fgr>
    \endverbatim  
  
    \param offset times the \p indent string must be used as a lead in the
    formatting of elements.

    \param indent string used to create the leading space that is placed
    at the beginning of indented XML elements inside the XML
    element. Defaults to two spaces(QString(" ")).

    \return a dynamically allocated string that needs to be freed after
    use.

    \sa renderXmlFgrElement(const QDomElement &element).
  */
  QString *
00475   FragRule::formatXmlFgrElement(int offset, const QString &indent)
  {
  
    int newOffset;
    int iter = 0;
  
    QString lead("");
    QString *string = new QString();
  

    // Prepare the lead.
    newOffset = offset;  
    while(iter < newOffset)
      {
      lead += indent;
      ++iter;
      }

    *string += QString("%1<fgr>\n")
      .arg(lead);
  
    // Prepare the lead.
    ++newOffset;
    lead.clear();
    iter = 0;
    while(iter < newOffset)
      {
      lead += indent;
      ++iter;
      }
  
    // Continue with indented elements.

    *string += QString("%1<name>%2</name>\n")
      .arg(lead)
      .arg(m_name);
  
    *string += QString("%1<formula>%2</formula>\n")
      .arg(lead)
      .arg(m_formula);
  
    if (!m_prevCode.isEmpty())  
      *string += QString("%1<prev-mnm-code>%2</prev-mnm-code>\n")
      .arg(lead)
      .arg(m_prevCode);

    if (!m_currCode.isEmpty())  
      *string += QString("%1<curr-mnm-code>%2</curr-mnm-code>\n")
      .arg(lead)
      .arg(m_currCode);

    if (!m_nextCode.isEmpty())
      *string += QString("%1<next-mnm-code>%2</next-mnm-code>\n")
      .arg(lead)
      .arg(m_nextCode);

    if (!m_comment.isEmpty())
      *string += QString("%1<comment>%2</comment>\n")
      .arg(lead)
      .arg(m_comment);

    // Prepare the lead.
    --newOffset;
    lead.clear();
    iter = 0;
    while(iter < newOffset)
      {
      lead += indent;
      ++iter;
      }
  
    *string += QString("%1</fgr>\n")
      .arg(lead);

  
    return string;
  }

} // namespace massXpert

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