/* BEGIN software license
 *
 * msXpertSuite - mass spectrometry software suite
 * -----------------------------------------------
 * Copyright(C) 2009,...,2018 Filippo Rusconi
 *
 * http://www.msxpertsuite.org
 *
 * This file is part of the msXpertSuite project.
 *
 * The msXpertSuite project is the successor of the massXpert project. This
 * project now includes various independent modules:
 *
 * - massXpert, model polymer chemistries and simulate mass spectrometric data;
 * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program 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 program. If not, see <http://www.gnu.org/licenses/>.
 *
 * END software license
 */


/////////////////////// Local includes
#include <massxpert/nongui/ChemicalGroup.hpp>


namespace msXpSmassXpert
{

ChemicalGroup::ChemicalGroup(QString name,
                             float pka,
                             bool acidCharged,
                             int polRule)
  : m_name(name), m_pka(pka), m_acidCharged(acidCharged), m_polRule(polRule)
{
  Q_ASSERT(m_pka > 0 && m_pka < 14);
}

ChemicalGroup::ChemicalGroup(const ChemicalGroup &other)
  : m_name(other.m_name),
    m_pka(other.m_pka),
    m_acidCharged(other.m_acidCharged),
    m_polRule(other.m_polRule)
{
}

ChemicalGroup::~ChemicalGroup()
{
  while(!m_ruleList.isEmpty())
    delete m_ruleList.takeFirst();
}

void
ChemicalGroup::setName(QString name)
{
  m_name = name;
}

QString
ChemicalGroup::name() const
{
  return m_name;
}

void
ChemicalGroup::setPka(float pka)
{
  Q_ASSERT(pka > 0 && pka < 14);

  m_pka = pka;
}

float
ChemicalGroup::pka() const
{
  return m_pka;
}

void
ChemicalGroup::setAcidCharged(bool acidCharged)
{
  m_acidCharged = acidCharged;
}

bool
ChemicalGroup::isAcidCharged() const
{
  return m_acidCharged;
}

void
ChemicalGroup::setPolRule(int polRule)
{
  m_polRule = polRule;
}

int
ChemicalGroup::polRule() const
{
  return m_polRule;
}

QList<ChemicalGroupRule *> &
ChemicalGroup::ruleList()
{
  return m_ruleList;
}

ChemicalGroupRule *
ChemicalGroup::findRuleEntity(QString value, int *index) const
{
  int ruleIndex = 0;

  if(!index)
    ruleIndex = 0;
  else
    {
      if(*index < 0)
        return 0;
      else if(*index > m_ruleList.size())
        return 0;
      ruleIndex = *index;
    }

  if(value.isEmpty())
    return 0;

  for(int iter = ruleIndex; iter < m_ruleList.size(); ++iter)
    {
      ChemicalGroupRule *rule = m_ruleList.at(iter);

      if(rule->entity() == value)
        {
          if(index)
            *index = iter;

          return rule;
        }
    }

  return 0;
}

ChemicalGroupRule *
ChemicalGroup::findRuleName(QString value, int *index) const
{
  int ruleIndex = 0;

  if(!index)
    ruleIndex = 0;
  else
    {
      if(*index < 0)
        return 0;
      else if(*index > m_ruleList.size())
        return 0;
      ruleIndex = *index;
    }

  if(value.isEmpty())
    return 0;

  for(int iter = ruleIndex; iter < m_ruleList.size(); ++iter)
    {
      ChemicalGroupRule *rule = m_ruleList.at(iter);

      if(rule->name() == value)
        {
          if(index)
            *index = iter;

          return rule;
        }
    }

  return 0;
}

ChemicalGroupRule *
ChemicalGroup::findRule(QString entity, QString name, int *index) const
{
  int ruleIndex = 0;

  if(!index)
    ruleIndex = 0;
  else
    {
      if(*index < 0)
        return 0;
      else if(*index > m_ruleList.size())
        return 0;
      ruleIndex = *index;
    }

  if(entity.isEmpty() || name.isEmpty())
    return 0;

  for(int iter = ruleIndex; iter < m_ruleList.size(); ++iter)
    {
      ChemicalGroupRule *rule = m_ruleList.at(iter);

      if(rule->entity() == entity && rule->name() == name)
        {
          if(index)
            *index = iter;

          return rule;
        }
    }

  return 0;
}

bool
ChemicalGroup::renderXmlMnmElement(const QDomElement &element)
{
  QDomElement child;

  // In an acidobasic definition file, the following xml structure
  // is encountered:

  // <acidobasicdata>
  //   <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>

  // The relevant DTD lines are:

  // <!ELEMENT monomer(code,mnmchemgroup*)>
  // <!ELEMENT mnmchemgroup(name,pka,acidcharged,polrule,chemgrouprule*)>

  // And the element the parameter points to is:

  //  <chemgroup>

  // Which means that element.tagName() == "chemgroup" 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.

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

  child = element.firstChildElement("name");

  if(child.isNull())
    return false;

  m_name = child.text();

  child = child.nextSiblingElement();

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

  bool ok = false;
  m_pka   = child.text().toFloat(&ok);

  if(!m_pka && !ok)
    return false;

  if(m_pka <= 0 || m_pka >= 14)
    return false;

  child = child.nextSiblingElement();

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

  if(child.text() != "FALSE" && child.text() != "TRUE")
    return false;

  m_acidCharged = (child.text() == "FALSE" ? false : true);

  // And now the polrule element. There should be one, here, in fact,
  // because we are dealing with a monomer, and not a modification.

  child = child.nextSiblingElement();

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

  if(child.text() == "never_trapped")
    m_polRule = CHEMGROUP_NEVER_TRAPPED;
  else if(child.text() == "left_trapped")
    m_polRule = CHEMGROUP_LEFT_TRAPPED;
  else if(child.text() == "right_trapped")
    m_polRule = CHEMGROUP_RIGHT_TRAPPED;
  else
    return false;

  // And finally the chemical group rules... There might be zero, one
  // or more.

  QDomElement childChemGroupRule = child.nextSiblingElement("chemgrouprule");

  while(!childChemGroupRule.isNull())
    {
      ChemicalGroupRule *rule = new ChemicalGroupRule();

      if(!rule->renderXmlElement(childChemGroupRule))
        {
          delete rule;
          return false;
        }

      m_ruleList.append(rule);

      childChemGroupRule = childChemGroupRule.nextSiblingElement();
    }

  return true;
}

bool
ChemicalGroup::renderXmlMdfElement(const QDomElement &element)
{
  QDomElement child;

  // In an acidobasic definition file, the following xml structure
  // is encountered:

  // <acidobasicdata>
  // <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>

  // The relevant DTD lines are:

  // <!ELEMENT modif(name,mdfchemgroup*)>
  // <!ELEMENT mdfchemgroup(name,pka,acidcharged)>

  // And the element the parameter points to is:

  //  <chemgroup>

  // Which means that element.tagName() == "chemgroup" 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.

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

  child = element.firstChildElement("name");

  if(child.isNull())
    return false;

  m_name = child.text();

  child = child.nextSiblingElement();

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

  bool ok = false;
  m_pka   = child.text().toFloat(&ok);

  if(!m_pka && !ok)
    return false;

  if(m_pka <= 0 || m_pka >= 14)
    return false;

  child = child.nextSiblingElement();

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

  if(child.text() != "FALSE" && child.text() != "TRUE")
    return false;

  m_acidCharged = (child.text() == "FALSE" ? false : true);

  return true;
}


//////////////////////// ChemicalGroupProp ////////////////////////

ChemicalGroupProp::ChemicalGroupProp(const QString &name, ChemicalGroup *data)
{
  if(!name.isEmpty())
    m_name = name;
  else
    m_name = QString();

  mpa_data = static_cast<void *>(data);
}

ChemicalGroupProp::~ChemicalGroupProp()
{
  deleteData();
}


//! Deletes the data in this double property.

/*! The data is destroyed as a double is destroyed.
 */
void
ChemicalGroupProp::deleteData()
{
  if(mpa_data)
    {
      delete static_cast<ChemicalGroup *>(mpa_data);
      mpa_data = 0;
    }
}

void *
ChemicalGroupProp::clone() const
{
  ChemicalGroupProp *prop = 0;

  if(mpa_data)
    prop =
      new ChemicalGroupProp(m_name, static_cast<ChemicalGroup *>(mpa_data));

  return static_cast<void *>(prop);
}

void
ChemicalGroupProp::cloneOut(void *other) const
{
  Q_ASSERT(other);

  ChemicalGroupProp *otherProp = static_cast<ChemicalGroupProp *>(other);

  if(otherProp->mpa_data)
    otherProp->deleteData();

  otherProp->m_name = m_name;

  ChemicalGroup *chemicalGroup = 0;

  if(mpa_data)
    {
      chemicalGroup = static_cast<ChemicalGroup *>(mpa_data);

      otherProp->mpa_data =
        static_cast<void *>(new ChemicalGroup(*chemicalGroup));
    }
  else
    otherProp->mpa_data = 0;
}

void
ChemicalGroupProp::cloneIn(const void *other)
{
  Q_ASSERT(other);

  const ChemicalGroupProp *otherProp =
    static_cast<const ChemicalGroupProp *>(other);

  if(mpa_data)
    deleteData();

  m_name = otherProp->m_name;

  ChemicalGroup *chemicalGroup = 0;

  if(otherProp->mpa_data)
    {
      chemicalGroup = static_cast<ChemicalGroup *>(otherProp->mpa_data);

      mpa_data = static_cast<void *>(new ChemicalGroup(*chemicalGroup));
    }
  else
    mpa_data = 0;
}

bool
ChemicalGroupProp::renderXmlElement(const QDomElement &element, int version)
{
  Q_UNUSED(element);
  Q_UNUSED(version);

  return false;
}

QString *
ChemicalGroupProp::formatXmlElement(int offset, const QString &indent)
{
  Q_UNUSED(offset);
  Q_UNUSED(indent);

  return nullptr;
}

} // namespace msXpSmassXpert
