Logo Search packages:      
Sourcecode: massxpert version File versions

cleaveRule.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 "cleaveRule.hpp"
#include "polChemDef.hpp"


namespace massXpert
{

  //! Construct a cleavage rule.
  /*! 
    \param polChemDef Polymer chemistry definition. Cannot be 0.

    \param name Name. Cannot be empty.

    \param leftCode Left code. Defaults to the null string.

    \param leftFormula Left formula. Defaults to the null string.

    \param rightCode Right code. Defaults to the null string.

    \param rightFormula Right formula. Defaults to the null string.
  */
00060   CleaveRule::CleaveRule(const PolChemDef *polChemDef,
                    QString name,
                    QString leftCode, 
                    QString leftFormula,
                    QString rightCode, 
                    QString rightFormula)
    : PolChemDefEntity(polChemDef, name),
      m_leftCode(leftCode), m_leftFormula(leftFormula),
      m_rightCode(rightCode), m_rightFormula(rightFormula)
  {
  }


  //! Constructs a copy of \p other.
  /*!  \param other cleavage rule to be used as a mold.
   */
00076   CleaveRule::CleaveRule(const CleaveRule &other)
    : PolChemDefEntity(other),
      m_leftCode(other.m_leftCode), m_leftFormula(other.m_leftFormula),
      m_rightCode(other.m_rightCode), m_rightFormula(other.m_rightFormula)
  {
  }


  //! Destroys the cleavage rule.
00085   CleaveRule::~CleaveRule()
  {
  }


  //! Modifies \p other to be identical to \p this.
  /*!  \param other cleavage rule.
   */
  void 
00094   CleaveRule::clone(CleaveRule *other)
  {
    Q_ASSERT(other);
  
    PolChemDefEntity::clone(other);
  
    other->m_leftCode = m_leftCode;
    m_leftFormula.clone(&other->m_leftFormula);
  
    other->m_rightCode = m_rightCode;
    m_rightFormula.clone(&other->m_rightFormula);
  }


  //! Modifies \p this  to be identical to \p other.
  /*!  \param other cleavage rule to be used as a mold.
   */
  void 
00112   CleaveRule::mold(const CleaveRule &other)
  { 
    if (&other == this)
      return;
  
    m_leftCode = other.m_leftCode;
    m_leftFormula.mold(other.m_leftFormula);
  
    m_rightCode = other.m_rightCode;
    m_rightFormula.mold(other.m_rightFormula);
  }


  //! Assigns other to \p this cleavage rule.
  /*! \param other cleavage rule used as the mold to set values to \p this
    instance.
  
    \return a reference to \p this cleavage rule.
  */
  CleaveRule &
00132   CleaveRule::operator =(const CleaveRule &other)
  {
    if (&other != this)
      mold(other);
  
    return *this;
  }




  //! Sets the left code.
  /*!  \param str new code.
   */
  void 
00147   CleaveRule::setLeftCode(const QString &str)
  {
    m_leftCode = str;
  }


  //! Returns the left code.
  /*!  \return the left code.
   */
  const QString &
00157   CleaveRule::leftCode()
  {
    return m_leftCode;
  }


  //! Sets the right code.
  /*!  \param str new code.
   */
  void 
00167   CleaveRule::setRightCode(const QString &str)
  {
    m_rightCode = str;
  }


  //! Returns the right code.
  /*!  \return the right code.
   */
  const QString &
00177   CleaveRule::rightCode()
  {
    return m_rightCode;
  }


  //! Sets the left formula.
  /*!  \param str new formula.
   */
  void 
00187   CleaveRule::setLeftFormula(const Formula &str)
  {
    m_leftFormula = str;
  }


  //! Returns the left formula.
  /*!  \return the left formula.
   */
  const Formula &
00197   CleaveRule::leftFormula()
  {
    return m_leftFormula;
  }


  //! Sets the right formula.
  /*!  \param str new formula.
   */
  void 
00207   CleaveRule::setRightFormula(const Formula &str)
  {
    m_rightFormula = str;
  }


  //! Returns the right formula.
  /*!  \return the right formula.
   */
  const Formula &
00217   CleaveRule::rightFormula()
  {
    return m_rightFormula;
  }


  int 
  CleaveRule::isNameInList(const QString &str, 
                      const QList<CleaveRule*> &refList,
                      CleaveRule *other)
  {
    CleaveRule *cleaveRule = 0;

    if (str.isEmpty())
      return -1;
  
    for (int iter = 0; iter < refList.size(); ++iter)
      {
      cleaveRule = refList.at(iter);
      Q_ASSERT(cleaveRule);

      if(cleaveRule->m_name == str)
        {
          if (other)
            cleaveRule->clone(other);
        
          return iter;
        }
      }
  
    return -1;
  }


  //! Validates the cleavage rule.
  /*!  \return true if validation is successful, false otherwise.
   */
  bool 
00255   CleaveRule::validate()
  {
    const QList<Monomer *> &monomerRefList = mp_polChemDef->monomerList();
    const QList<Atom *> &atomRefList = mp_polChemDef->atomList();
  
    if (!m_leftCode.isEmpty())
      {
      if(Monomer::isCodeInList(m_leftCode, monomerRefList) == -1)
        return false;
      
      if(m_leftFormula.formula().isEmpty())
        return false;
      
      if(!m_leftFormula.validate(atomRefList))
        return false;
      }
  
    if (!m_rightCode.isEmpty())
      {
      if(Monomer::isCodeInList(m_rightCode, monomerRefList) == -1)
        return false;
      
      if(m_rightFormula.formula().isEmpty())
        return false;
      
      if(!m_rightFormula.validate(atomRefList))
        return false;
      }

    return true;
  }



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

    \sa formatXmlClrElement(int offset, const QString &indent).
  */
  bool 
00302   CleaveRule::renderXmlClrElement(const QDomElement &element, int version)
  {
    QDomElement child;

    bool leftCodeSet = false;
    bool leftFormulaSet = false;
    bool rightCodeSet = false;
    bool rightFormulaSet = false;

    /* The xml node we are in is structured this way:
     *
     *  <clr>
     *     <name>Homeseryl</name>
     *     <le-mnm-code>M</le-mnm-code>
     *     <le-formula>-C1H2S1+O1</le-formula>
     *     <re-mnm-code>M</re-mnm-code>
     *     <re-formula>-C1H2S1+O1</re-formula>
     *  </clr>
     *
     * And the element parameter points to the 
     *
     * <clr> element tag:
     *  ^
     *  |
     *  +----- here we are right now.
     * 
     * Which means that xml_node->name == "clr" and that
     * we'll have to go one step down to the first child of the 
     * current node in order to get to the <code> element.
     *
     * Note that the DTD stipulates that there can be no or one at most
     * of each left end and/or right end set of data. So be careful 
     * with the assertions !
     * This is the DTD material:
     * <!ELEMENT clr((le-mnm-code,le-formula)?,
     *(re-mnm-code,re-formula)?)>
     */

    if (element.tagName() != "clr")
      return false;
  
    child = element.firstChildElement();
  
    // If version is at least 3, then the next element has to be "name".
    if (version >= 3)
      {
      if(child.tagName() != "name")
        return false;
      
      m_name = child.text();

      child = child.nextSiblingElement();
      }

    // It cannot be that there is nothing in this element!
    while(!child.isNull())
      {
      // OK, apparently there is a child element, so let's try to see
      // what's going on. It can either be "le-mnm-code" or "re-mnm-code".
      
      if(child.tagName() == "le-mnm-code")
        {
          m_leftCode = child.text();
          leftCodeSet = true;
        }
      else if (child.tagName() == "le-formula")
        {
          m_leftFormula.setFormula(child.text());
          leftFormulaSet = true;
        }
      else if (child.tagName() == "re-mnm-code")
        {
          m_rightCode = child.text();
          rightCodeSet = true;
        }
      else if (child.tagName() == "re-formula")
        {
          m_rightFormula.setFormula(child.text());
          rightFormulaSet = true;
        }

      child = child.nextSiblingElement();
      }

    // OK, we just finished parsing this <clr> element. Check what we
    // got.

    if (leftCodeSet)
      {
      if(!leftFormulaSet)
        return false;
      }

    if (rightCodeSet)
      {
      if(!rightFormulaSet)
        return false;
      }
  
    // It cannot be that no single code could be set.
    if (!leftCodeSet && !rightCodeSet)
      return false;
  
    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 cleavage rule element
    that is generated in this function looks like this:

    \verbatim 
    <clr>
    <re-mnm-code>M</re-mnm-code>
    <re-formula>-CH2S+O</re-formula>
    </clr>
    \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 renderXmlClrElement(const QDomElement &element).
  */
  QString *
00437   CleaveRule::formatXmlClrElement(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;
      }

    /*
      <clr>
      <re-mnm-code>M</re-mnm-code>
      <re-formula>-CH2S+O</re-formula>
      </clr>
    */

    *string += QString("%1<clr>\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);

    if (!m_leftCode.isEmpty())
      {
      Q_ASSERT(!m_leftFormula.formula().isEmpty());
      
      *string += QString("%1<le-mnm-code>%2</le-mnm-code>\n")
        .arg(lead)
        .arg(m_leftCode);

      *string += QString("%1<le-formula>%2</le-formula>\n")
        .arg(lead)
        .arg(m_leftFormula.formula());
      }
  
    if (!m_rightCode.isEmpty())
      {
      Q_ASSERT(!m_rightFormula.formula().isEmpty());
      
      *string += QString("%1<re-mnm-code>%2</re-mnm-code>\n")
        .arg(lead)
        .arg(m_rightCode);
      
      *string += QString("%1<re-formula>%2</re-formula>\n")
        .arg(lead)
        .arg(m_rightFormula.formula());
      }

    // Prepare the lead for the closing element.
    --newOffset;
    lead.clear();
    iter = 0;
    while(iter < newOffset)
      {
      lead += indent;
      ++iter;
      }

    *string += QString("%1</clr>\n")
      .arg(lead);
  
    return string;
  }

} // namespace massXpert

Generated by  Doxygen 1.6.0   Back to index