/* 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 "pkaPhPiDataParser.hpp"
#include "chemicalGroup.hpp"


namespace massXpert
{

  PkaPhPiDataParser::PkaPhPiDataParser(const PolChemDef *polChemDef,
					QString filePath)
    : mp_polChemDef(polChemDef), m_filePath(filePath)
  {
    Q_ASSERT(mp_polChemDef);
  }


  PkaPhPiDataParser::~PkaPhPiDataParser()
  {
  
  }

  
  void 
  PkaPhPiDataParser::setFilePath(const QString &filePath)
  {
    m_filePath = filePath;
  }


  const QString &
  PkaPhPiDataParser::filePath()
  {
    return m_filePath;
  }


  bool
  PkaPhPiDataParser::renderXmlFile(QList<Monomer *> *monomerList,
				    QList<Modif *> *modifList)
  {
    Q_ASSERT(monomerList);
    Q_ASSERT(modifList);

    // General structure of the file:
    // 
    // <pkaphpidata>
    //   <monomers>
    //     <monomer>
    //       <code>A</code>
    //       <mnmchemgroup>
    //         <name>N-term NH2</name>
    // 	<pka>9.6</pka>
    // 	<acidcharged>TRUE</acidcharged>
    // 	<polrule>left_trapped</polrule>
    // 	<chemgrouprule>
    // 	  <entity>LE_PLM_MODIF</entity>
    // 	  <name>Acetylation</name>
    // 	  <outcome>LOST</outcome>
    // 	</chemgrouprule>
    //       </mnmchemgroup>
    //       <mnmchemgroup>
    //         <name>C-term COOH</name>
    // 	<pka>2.35</pka>
    // 	<acidcharged>FALSE</acidcharged>
    // 	<polrule>right_trapped</polrule>
    //       </mnmchemgroup>
    //    </monomer>
    // ...
    // 
    //   <modifs>
    //     <modif>
    //       <name>Phosphorylation</name>
    //       <mdfchemgroup>
    //         <name>none_set</name>
    // 	<pka>12</pka>
    // 	<acidcharged>FALSE</acidcharged>
    //       </mdfchemgroup>
    //       <mdfchemgroup>
    //         <name>none_set</name>
    // 	<pka>7</pka>
    // 	<acidcharged>FALSE</acidcharged>
    //       </mdfchemgroup>
    //     </modif>
    //   </modifs>
    // </pkaphpidata>
    // 
    // The DTD stipulates that:
    //
    // <!ELEMENT pkaphpidata(monomers,modifs*)>
    // <!ELEMENT monomers(monomer*)>
    // <!ELEMENT modifs(modif*)>
    // <!ELEMENT monomer(code,mnmchemgroup*)>
    // <!ELEMENT modif(name,mdfchemgroup*)>


    QDomDocument doc("pkaPhPiData");
    QDomElement element;  
    QDomElement child;
    QDomElement indentedChild;
  
    QFile file(m_filePath);

    if (!file.open(QIODevice::ReadOnly))
      return false;
  
    if (!doc.setContent(&file)) 
      {
	file.close();
	return false;
      }
  
    file.close();

    element = doc.documentElement();

    if (element.tagName() != "pkaphpidata")
      {
	qDebug() << __FILE__ << __LINE__ 
		  << "pKa-pH-pI data file is erroneous\n";
	return false;
      }
  
    // The first child element must be <monomers>.

    child = element.firstChildElement();
    if (child.tagName() != "monomers")
      {
	qDebug() << __FILE__ << __LINE__ 
		  << "pKa-pH-pI data file is erroneous\n";
	return false;
      }
  
    // Parse the <monomer> elements.

    indentedChild = child.firstChildElement();
    while(!indentedChild.isNull())
      {
	if(indentedChild.tagName() != "monomer")
	  return false;
      
	QDomElement superIndentedElement = indentedChild.firstChildElement();

	if(superIndentedElement.tagName() != "code")
	  return false;
      
	Monomer *monomer = new Monomer(mp_polChemDef, "NOT_SET",
					superIndentedElement.text());
      
	// All the <mnmchemgroup> elements, if any.

	superIndentedElement = superIndentedElement.nextSiblingElement();
	while(!superIndentedElement.isNull())
	  {
	    if (superIndentedElement.tagName() != "mnmchemgroup")
	      {
		delete monomer;
		return false;
	      }
	  
	    ChemicalGroup *chemGroup = new ChemicalGroup("NOT_SET");
	  
	    if (!chemGroup->renderXmlMnmElement(superIndentedElement))
	      {
		delete monomer;
		delete chemGroup;
		return false;
	      }
	  
	    ChemicalGroupProp *prop =
	      new ChemicalGroupProp("CHEMICAL_GROUP", chemGroup);
	  
	    monomer->appendProp(prop);
	  
	    superIndentedElement = superIndentedElement.nextSiblingElement();
	  }

	monomerList->append(monomer);

	indentedChild = indentedChild.nextSiblingElement();
      }
  
#if 0

    qDebug() << __FILE__ << __LINE__ 
	      << "Debug output of all the monomers parsed:";
  
    for (int iter = 0; iter < monomerList->size(); ++iter)
      {
	Monomer *monomer = monomerList->at(iter);
	qDebug() << __FILE__ << __LINE__ 
		  << "Monomer:" << monomer->name();
      
	for(int jter = 0; jter < monomer->propList()->size(); ++jter)
	  {
	    Prop *prop = monomer->propList()->at(jter);
	  
	    if (prop->name() == "CHEMICAL_GROUP")
	      {
		const ChemicalGroup *chemGroup = 
		  static_cast<const ChemicalGroup *>(prop->data());
	      
		qDebug() << __FILE__ << __LINE__ 
			  << "Chemical group:"
			  << chemGroup->name() << chemGroup->pka();
	      }
	  }
      }
  
#endif  

    // And now parse the <modifs> elements, if any, this time, as
    // this element is not compulsory.
  
    child = child.nextSiblingElement();
    if (child.isNull())
      return true;
  
    if (child.tagName() != "modifs")
      {
	qDebug() << __FILE__ << __LINE__ 
		  << "pKa-pH-pI data file is erroneous\n";
	return false;
      }

    // Parse the <modif> elements.
  
    indentedChild = child.firstChildElement();
    while(!indentedChild.isNull())
      {
	if(indentedChild.tagName() != "modif")
	  return false;
      
	QDomElement superIndentedElement = indentedChild.firstChildElement();
      
	if(superIndentedElement.tagName() != "name")
	  return false;
      
	Modif *modif = 
	  new Modif(mp_polChemDef, superIndentedElement.text(), "H0");
      
	// All the <mdfchemgroup> elements, if any.
      
	superIndentedElement = superIndentedElement.nextSiblingElement();
	while(!superIndentedElement.isNull())
	  {
	    if (superIndentedElement.tagName() != "mdfchemgroup")
	      {
		delete modif;
		return false;
	      }
	  
	    ChemicalGroup *chemGroup = new ChemicalGroup("NOT_SET");
	  
	    if (!chemGroup->renderXmlMdfElement(superIndentedElement))
	      {
		delete modif;
		delete chemGroup;
		return false;
	      }
	  
	    ChemicalGroupProp *prop =
	      new ChemicalGroupProp("CHEMICAL_GROUP", chemGroup);
	  
	    modif->appendProp(prop);
	  
	    superIndentedElement = superIndentedElement.nextSiblingElement();
	  }

	modifList->append(modif);

	indentedChild = indentedChild.nextSiblingElement();
      }

#if 0

    qDebug() << __FILE__ << __LINE__ 
	      << "Debug output of all the modifs parsed:";
  
    for (int iter = 0; iter < modifList->size(); ++iter)
      {
	Modif *modif = modifList->at(iter);

	//       qDebug() << __FILE__ << __LINE__ 
	// 		<< "Modif:" << modif->name();
      
	for(int jter = 0; jter < modif->propList()->size(); ++jter)
	  {
	    Prop *prop = modif->propList()->at(jter);
	  
	    if (prop->name() == "CHEMICAL_GROUP")
	      {
		const ChemicalGroup *chemGroup = 
		  static_cast<const ChemicalGroup *>(prop->data());
	      
		qDebug() << __FILE__ << __LINE__ 
			  << "Chemical group:"
			  << chemGroup->name() << chemGroup->pka();
	      }
	  }
      }
  
#endif
  
    return true;
  }

} // namespace massXpert