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crossLinker.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 "crossLinker.hpp"
#include "polChemDef.hpp"


namespace massXpert
{

  CrossLinker::CrossLinker(const PolChemDef *polChemDef,
                      const QString &name, 
                      const QString &formula)
    : PolChemDefEntity(polChemDef, name),
      Formula(formula)
  {
  }


  CrossLinker::CrossLinker(const CrossLinker &other)
    : PolChemDefEntity(other), Formula(other), Ponderable(other)
  {
    for (int iter = 0 ; iter < other.m_modifList.size() ; ++iter)
      m_modifList.append(other.m_modifList.at(iter));
  }


  CrossLinker::~CrossLinker()
  {
    // We do not own the modifications in m_modifList!
  }

  
  CrossLinker *
  CrossLinker::clone() const
  {
    CrossLinker *other = new CrossLinker(*this);
  
    return other;
  }


  void 
  CrossLinker::clone(CrossLinker *other) const
  {
    Q_ASSERT(other);
  
    PolChemDefEntity::clone(other);
    Formula::clone(other);
    Ponderable::clone(other);

    // Empty other's list of modifs. Do not delete them, we do not own
    // them.
    while(!other->m_modifList.isEmpty())
      other->m_modifList.removeFirst();
  
    for (int iter = 0 ; iter < m_modifList.size() ; ++iter)
      other->m_modifList.append(m_modifList.at(iter));
  }


  bool
  CrossLinker::setModifAt(Modif *modif, int index)
  {
    Q_ASSERT(modif);
    Q_ASSERT(index >= 0 && index < m_modifList.size());
    
    m_modifList.replace(index, modif);
  
    return true;
  }


  bool
  CrossLinker::appendModif(Modif *modif)
  {
    Q_ASSERT(modif);
    m_modifList.append(modif);
  
    return true;
  }


  const Modif *
  CrossLinker::modifAt(int index) const
  {
    Q_ASSERT(index >= 0 && index < m_modifList.size());
  
    return m_modifList.at(index);
  }


  bool 
  CrossLinker:: removeModifAt(int index)
  {
    Q_ASSERT(index < m_modifList.size());

    m_modifList.removeAt(index);

    return true;
  }


  QList<Modif *> &
  CrossLinker::modifList()
  {
    return m_modifList;
  }

  
  int 
  CrossLinker::hasModif (const QString &modifName)
  {
    // Iterate in the list of modifications, and check if one of these
    // has the name passed as argument. If so return the index of the
    // found item in the list, otherwise return -1.

    for (int iter = 0; iter < m_modifList.size(); ++iter)
      {
      Modif *modif = m_modifList.at(iter);
      
      if (modif->name() == modifName)
        return iter;
      }
    
    return -1;
  }
  

  bool
  CrossLinker::operator ==(const CrossLinker &other) const
  {
    int tests = 0;
  
    tests += PolChemDefEntity::operator ==(other);
    tests += Formula::operator ==(other);
    tests += Ponderable::operator ==(other);
  
    if (m_modifList.size() != other.m_modifList.size())
      return false;
  
    for (int iter = 0; iter < m_modifList.size(); ++iter)
      {
      if(m_modifList.at(iter) != other.m_modifList.at(iter))
        return false;
      }
    
    if (tests < 3)
      return false;
    else 
      return true;
  }
 

  int 
  CrossLinker::isNameKnown()
  {
    const QList<CrossLinker*> &refList = mp_polChemDef->crossLinkerList();
  
    if (m_name.isEmpty())
      return -1;
  
    for (int iter = 0 ; iter < refList.size() ; ++iter)
      {
      if(refList.at(iter)->m_name == m_name)
        return iter;
      }

    return -1;
  }


  int 
  CrossLinker::isNameInList(const QString &name, 
                       const QList<CrossLinker*> &refList,
                       CrossLinker *other)
  {
    CrossLinker *crossLinker = 0;
  
    if (name.isEmpty())
      return -1;
  
    for (int iter = 0; iter < refList.size(); ++iter)
      {
      crossLinker = refList.at(iter);
      Q_ASSERT(crossLinker);
      
      if(crossLinker->m_name == name)
        {
          if (other)
            crossLinker->clone(other);
        
          return iter;
        }
      }
  
    return -1;  
  }


  bool 
  CrossLinker::validate()
  {
    if (!mp_polChemDef)
      return false;
  
    if (m_name.isEmpty())
      return false;
    
    Formula formula(m_formula);
    const QList<Atom *> &refList = mp_polChemDef->atomList();
  
    if (!formula.validate(refList))
      return false;

    // This is mainly a sanity check, as the pointers to Modif in the
    // list all point to modification objects in the polymer chemistry
    // definition, which have been validated already...
  
    // The validation actually is simple, it might be that there are NO
    // modifs, or if this is not the case there must be at least
    // 2. Indeed, either none of the monomers in the crosslink get
    // modified, or each one has to be(otherwise we cannot know which
    // modif goes to which monomer).

    int size = m_modifList.size();
  
    if (size > 0 && size < 2)
      return false;
  
    for (int iter = 0; iter < size; ++iter)
      {
      // Make sure the modification is known to the polymer chemistry
      // definition. This check is not performed by the modif's
      // validation function.

      if(!mp_polChemDef->modif(m_modifList.at(iter)->name()))
        return false;
      
      if(!m_modifList.at(iter)->validate())
        return false;
      }
  
    return true;
  }


  bool 
  CrossLinker::calculateMasses()
  {
    const QList<Atom *> &refList = mp_polChemDef->atomList();
  
    m_mono = 0;
    m_avg = 0;
  
    // Account the masses of the formula parent class.
    if (!Formula::accountMasses(refList, &m_mono, &m_avg))
      return false;

    // Now, for each modif in the crossLinker, have to account their
    // mass.
  
    for (int iter = 0; iter < m_modifList.size(); iter ++)
      {
      Modif *modif = m_modifList.at(iter);
      
      if(!modif->accountMasses(&m_mono, &m_avg))
        return false;
      }
        
    return true;
  }


  bool 
  CrossLinker::accountMasses(double *mono, double *avg, int times)
  {
    if (mono)
      *mono += m_mono * times;
  
    if (avg)
      *avg += m_avg * times;
  
    return true;
  }


  bool 
  CrossLinker::accountMasses(Ponderable *ponderable, int times)
  {
    Q_ASSERT(ponderable);
  
    ponderable->rmono() += m_mono * times;
    ponderable->ravg() += m_avg * times;

    return true;
  }


  bool  
  CrossLinker::renderXmlClkElement(const QDomElement &element, int version)
  {
    QDomElement child;

    if (element.tagName() != "clk")
      return false;

    if (version <= 3)
      return renderXmlClkElement(element);
    else if (version > 3)
      return renderXmlClkElementV3(element);

    return false;  
  }


  bool  
  CrossLinker::renderXmlClkElement(const QDomElement &element)
  {
    QDomElement child;
  
    if (element.tagName() != "clk")
      return false;

    child = element.firstChildElement("name");
  
    if (child.isNull())
      return false;
  
    m_name = child.text();
    if (m_name.isEmpty())
      return false;
    
    child = child.nextSiblingElement("formula");
  
    if (child.isNull())
      return false;
  
    if (!Formula::renderXmlFormulaElement(child))
      return false;
  
    const QList<Modif*> &refList = mp_polChemDef->modifList();

    // At this point there might be 0, 1 or more "modifname" elements.
    child = child.nextSiblingElement("modifname");

    while(!child.isNull())
      {
      int index = Modif::isNameInList(child.text(), refList);
      
      if(index == -1)
        {
          qDebug() << __FILE__ << __LINE__ 
                  << "Failed to parse one modification of the crosslink:"
                  << m_name;
        
          return false;
        }

      m_modifList.append(mp_polChemDef->modifList().at(index));

      child = child.nextSiblingElement("modifname");
      }

    if (!calculateMasses())
      {
      qDebug() << __FILE__ << __LINE__ 
              << "Failed to calculate masses for crossLinker" 
              << m_name;

      return false;
      }
  
    if (!validate())
      return false;
  
    return true;
  }



  bool  
  CrossLinker::renderXmlClkElementV3(const QDomElement &element)
  {
    // For the moment we do not use this version of the function.
    //  qDebug() << __FILE__ << __LINE__ << "Using version 3 function";
    return renderXmlClkElement(element);
  
  }


  QString * 
  CrossLinker::formatXmlClkElement(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;
      }

    /* We are willing to create an <modif> node that should look like this:
     *
     <clk>
     <name>Phosphorylation</name>
     <formula>-H+H2PO3</formula>
     <modifname>Phosphorylation</modifname>
     <modifname>Acetylation</modifname>
     </clk>
     *
     */

    *string += QString("%1<clk>\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);
    
    for (int iter = 0; iter < m_modifList.size() ; ++iter)
      {
      *string += QString("%1<modifname>%2</modifname>\n")
        .arg(lead)
        .arg(m_modifList.at(iter)->name());
      }
  
    // Prepare the lead for the closing element.
    --newOffset;
    lead.clear();
    iter = 0;
    while(iter < newOffset)
      {
      lead += indent;
      ++iter;
      }

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

} // namespace massXpert

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