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atomDefDlg.cpp

/* massXpert - the true massist's program.
   --------------------------------------
   Copyright(C) 2006,2007 Filippo Rusconi

   http://www.filomace.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.
*/


/////////////////////// Qt includes
#include <QMessageBox>


/////////////////////// Local includes
#include "application.hpp"
#include "atomDefDlg.hpp"
#include "polChemDef.hpp"
#include "polChemDefWnd.hpp"


namespace massXpert
{

  AtomDefDlg::AtomDefDlg(PolChemDef *polChemDef, 
                    PolChemDefWnd *polChemDefWnd)
  {
    Q_ASSERT(polChemDef);
    mp_polChemDef = polChemDef;
    mp_list = polChemDef->atomListPtr();
  
    Q_ASSERT(polChemDefWnd);
    mp_polChemDefWnd = polChemDefWnd;
  
    if (!initialize())
      {
      qDebug() << "Failed to initialize the atom definition window";
      }
  }


  void 
  AtomDefDlg::closeEvent(QCloseEvent *event)
  {  
    // No real close, because we did not ask that
    // close==destruction. Thus we only hide the dialog remembering its
    // position and size.
  
  
    mp_polChemDefWnd->m_ui.atomPushButton->setChecked(false);

    QSettings settings 
     (static_cast<Application *>(qApp)->configSettingsFilePath(), 
       QSettings::IniFormat);
  
    settings.beginGroup("atom_def_dlg");

    settings.setValue("geometry", saveGeometry());

    settings.setValue("splitter", m_ui.splitter->saveState());

    settings.endGroup();
  }

  

  AtomDefDlg::~AtomDefDlg()
  {
  }

  
  bool
  AtomDefDlg::initialize()
  {
    m_ui.setupUi(this);

    // Set all the atoms to the list widget.

    for (int iter = 0; iter < mp_list->size(); ++iter)
      {
      Atom *atom = mp_list->at(iter);
      
      m_ui.atomListWidget->addItem(atom->name());
      }

    QSettings settings 
     (static_cast<Application *>(qApp)->configSettingsFilePath(), 
       QSettings::IniFormat);
  
    settings.beginGroup("atom_def_dlg");

    restoreGeometry(settings.value("geometry").toByteArray());

    m_ui.splitter->restoreState(settings.value("splitter").toByteArray());
    
    settings.endGroup();


    // Validator stuff for the atom symbol lineedit.
    QRegExp symbolRegExp("[A-Z][a-z]*");
    QValidator *validator = new QRegExpValidator(symbolRegExp, this);

    m_ui.symbolLineEdit->setValidator(validator);


    // Make the connections.

    connect(m_ui.addAtomPushButton, 
           SIGNAL(clicked()),
           this, 
           SLOT(addAtomPushButtonClicked()));
  
    connect(m_ui.removeAtomPushButton, 
           SIGNAL(clicked()),
           this, 
           SLOT(removeAtomPushButtonClicked()));
  
    connect(m_ui.moveUpAtomPushButton, 
           SIGNAL(clicked()),
           this, 
           SLOT(moveUpAtomPushButtonClicked()));
  
    connect(m_ui.moveDownAtomPushButton, 
           SIGNAL(clicked()),
           this, 
           SLOT(moveDownAtomPushButtonClicked()));
  
    connect(m_ui.addIsotopePushButton, 
           SIGNAL(clicked()),
           this, 
           SLOT(addIsotopePushButtonClicked()));
  
    connect(m_ui.removeIsotopePushButton, 
           SIGNAL(clicked()),
           this, 
           SLOT(removeIsotopePushButtonClicked()));
  
    connect(m_ui.moveUpIsotopePushButton, 
           SIGNAL(clicked()),
           this, 
           SLOT(moveUpIsotopePushButtonClicked()));
  
    connect(m_ui.moveDownIsotopePushButton, 
           SIGNAL(clicked()),
           this, 
           SLOT(moveDownIsotopePushButtonClicked()));
  
    connect(m_ui.applyAtomPushButton, 
           SIGNAL(clicked()),
           this, 
           SLOT(applyAtomPushButtonClicked()));
  
    connect(m_ui.applyIsotopePushButton, 
           SIGNAL(clicked()),
           this, 
           SLOT(applyIsotopePushButtonClicked()));
  
    connect(m_ui.validatePushButton, 
           SIGNAL(clicked()),
           this, 
           SLOT(validatePushButtonClicked()));

    connect(m_ui.atomListWidget, 
           SIGNAL(itemSelectionChanged()),
           this, 
           SLOT(atomListWidgetItemSelectionChanged()));
  
    connect(m_ui.isotopeListWidget, 
           SIGNAL(itemSelectionChanged()),
           this, 
           SLOT(isotopeListWidgetItemSelectionChanged()));
  
    return true;
  }


  void 
  AtomDefDlg::addAtomPushButtonClicked()
  {
    // We are asked to add a new atom. We'll add it right after the
    // current item.
  
    // Returns -1 if the list is empty.
    int index = m_ui.atomListWidget->currentRow();
  
    Atom *newAtom = new Atom(tr("Type Name"),
                        tr("Type Symbol"));
  
    mp_list->insert(index, newAtom);
    m_ui.atomListWidget->insertItem(index, newAtom->name());

    setModified();
  
    // Needed so that the setCurrentRow() call below actually set the
    // current row!
    if (index <= 0)
      index = 0;
  
    m_ui.atomListWidget->setCurrentRow(index);

    // Erase isotope data that might be left over by precedent current
    // atom.
    updateIsotopeDetails(0);

    // Set the focus to the lineEdit that holds the name of the atom.
    m_ui.nameLineEdit->setFocus();
    m_ui.nameLineEdit->selectAll();
  }


  void 
  AtomDefDlg::removeAtomPushButtonClicked()
  {
    QList<QListWidgetItem *> selectedList = 
      m_ui.atomListWidget->selectedItems();
  
    if (selectedList.size() != 1)
      return;

    // Get the index of the current atom.
    int index = m_ui.atomListWidget->currentRow();
  
    QListWidgetItem *item = m_ui.atomListWidget->takeItem(index);
    delete item;

    Atom *atom = mp_list->takeAt(index);
    Q_ASSERT(atom);
    delete atom;
  
    setModified();
  
    // If there are remaining items, we want to set the next item the
    // currentItem. If not, then, the currentItem should be the one
    // preceding the atom that we removed.

    if (m_ui.atomListWidget->count() >= index + 1)
      {
      m_ui.atomListWidget->setCurrentRow(index);
      atomListWidgetItemSelectionChanged();
      }
  
    // If there are no more items in the atom list, remove all the items
    // from the isotopeList.
  
    if (!m_ui.atomListWidget->count())
      {
      m_ui.isotopeListWidget->clear();
      clearAllDetails();
      }
  }


  void 
  AtomDefDlg::moveUpAtomPushButtonClicked()
  {
    // Move the current row to one index less.

    // If no atom is selected, just return.

    QList<QListWidgetItem *> selectedList = 
      m_ui.atomListWidget->selectedItems();
  
    if (selectedList.size() != 1)
      return;

    // Get the index of the atom and the atom itself. 
    int index = m_ui.atomListWidget->currentRow();

    // If the item is already at top of list, do nothing.
    if (!index)
      return;

    mp_list->move(index, index - 1);

    QListWidgetItem *item = m_ui.atomListWidget->takeItem(index);

    m_ui.atomListWidget->insertItem(index - 1, item);
    m_ui.atomListWidget->setCurrentRow(index - 1);
    atomListWidgetItemSelectionChanged();

    setModified();
  }


  void 
  AtomDefDlg::moveDownAtomPushButtonClicked()
  {
    // Move the current row to one index less.

    // If no atom is selected, just return.

    QList<QListWidgetItem *> selectedList = 
      m_ui.atomListWidget->selectedItems();
  
    if (selectedList.size() != 1)
      return;

    // Get the index of the atom and the atom itself. 
    int index = m_ui.atomListWidget->currentRow();

    // If the item is already at bottom of list, do nothing.
    if (index == m_ui.atomListWidget->count() - 1)
      return;

    mp_list->move(index, index + 1);

    QListWidgetItem *item = m_ui.atomListWidget->takeItem(index);
    m_ui.atomListWidget->insertItem(index + 1, item);
    m_ui.atomListWidget->setCurrentRow(index + 1);
    atomListWidgetItemSelectionChanged();

    setModified();
  }


  void 
  AtomDefDlg::addIsotopePushButtonClicked()
  {
    Application *application = static_cast<Application *>(qApp);
    QLocale locale = application->locale();

    // We are asked to add a new isotope. We'll add it right after the
    // current item. Note however, that one atom has to be selected.
  
    QList<QListWidgetItem *> selectedList = 
      m_ui.atomListWidget->selectedItems();
  
    if (selectedList.size() != 1)
      {
      QMessageBox::information(this, 
                          tr("massXpert - Atom definition"),
                          tr("Please, select an atom first."),
                          QMessageBox::Ok);
      return;
      }
  
    // Get the index of the current atom so that we know to which atom
    // we'll add the isotope.
    int index = m_ui.atomListWidget->currentRow();
  
    // What's the actual atom?
    Atom *atom = mp_list->at(index);
    Q_ASSERT(atom);

    // Allocate the new isotope.
    Isotope *newIsotope = new Isotope();

    // Get the row index of the current isotope item. Returns -1 if the
    // list is empty.
    index = m_ui.isotopeListWidget->currentRow();
  
    m_ui.isotopeListWidget->insertItem(index, newIsotope->mass(locale));

    // Needed so that the setCurrentRow() call below actually set the
    // current row!
    if (index <= 0)
      index = 0;
  
    atom->insertIsotopeAt(index, newIsotope);
  
    m_ui.isotopeListWidget->setCurrentRow(index);

    setModified();

    // Set the focus to the lineEdit that holds the mass of the isotope.
    m_ui.isotopeMassLineEdit->setFocus();
    m_ui.isotopeMassLineEdit->selectAll();
  }


  void 
  AtomDefDlg::removeIsotopePushButtonClicked()
  {
    QList<QListWidgetItem *> selectedList = 
      m_ui.isotopeListWidget->selectedItems();
  
    if (selectedList.size() != 1)
      return;

  
    // Get the index of the current atom so that we know from which atom
    // we'll remove the isotope.
    int index = m_ui.atomListWidget->currentRow();
  
    Atom *atom = mp_list->at(index);
    Q_ASSERT(atom);

    // Get the index of the current isotope.
    index = m_ui.isotopeListWidget->currentRow();

    // First remove the item from the listwidget because that will have
    // isotopeListWidgetItemSelectionChanged() triggered and we have to
    // have the item in the isotope list in the atom! Otherwise a crash
    // occurs.
    QListWidgetItem *item = m_ui.isotopeListWidget->takeItem(index);
    delete item;

    // Remove the isotope from the atom proper.
  
    QList<Isotope *> atomIsotopeList = atom->isotopeList();
  
    Isotope *isotope = atomIsotopeList.at(index);
  
    atom->removeIsotopeAt(index);
    delete isotope;
   
    // If there are remaining items, we want to set the next item the
    // currentItem. If not, then, the currentItem should be the one
    // preceding the atom that we removed.

    if (m_ui.isotopeListWidget->count() >= index + 1)
      {
      m_ui.isotopeListWidget->setCurrentRow(index);
      isotopeListWidgetItemSelectionChanged();
      }
  
    // We have changed the isotopic constitution of the chemical
    // element, we have to recompute the mono/avg masses.

    atom->calculateMasses();

    // If there are no more items in the isotope list, remove all the
    // details.
  
    if (!m_ui.isotopeListWidget->count())
      {
      updateAtomMassDetails(0);
      updateIsotopeDetails(0);
      }
    else
      {
      updateAtomMassDetails(atom);
      }

    setModified();
  }
 

  void 
  AtomDefDlg::moveUpIsotopePushButtonClicked()
  {
    // Move the current row to one index less.

    // If no isotope is selected, just return.

    QList<QListWidgetItem *> selectedList = 
      m_ui.isotopeListWidget->selectedItems();
  
    if (selectedList.size() != 1)
      return;

    // Get the atom to which the isotope belongs. 
    int index = m_ui.atomListWidget->currentRow();
    Atom *atom = mp_list->at(index);

    // Get the index of the current isotope item.
    index = m_ui.isotopeListWidget->currentRow();
  
    // If the item is already at top of list, do nothing.
    if (!index)
      return;
  
    // Get the isotope itself from the atom.
    Isotope *isotope = atom->isotopeList().at(index);
  
    atom->removeIsotopeAt(index);
    atom->insertIsotopeAt(index - 1, isotope);

    QListWidgetItem *item = m_ui.isotopeListWidget->takeItem(index);
    m_ui.isotopeListWidget->insertItem(index - 1, item);
    m_ui.isotopeListWidget->setCurrentRow(index - 1);
    isotopeListWidgetItemSelectionChanged();

    setModified();
  }


  void 
  AtomDefDlg::moveDownIsotopePushButtonClicked()
  {
    // Move the current row to one index less.

    // If no isotope is selected, just return.

    QList<QListWidgetItem *> selectedList = 
      m_ui.isotopeListWidget->selectedItems();
  
    if (selectedList.size() != 1)
      return;

    // Get the atom to which the isotope belongs. 
    int index = m_ui.atomListWidget->currentRow();
    Atom *atom = mp_list->at(index);

    // Get the index of the current isotope item.
    index = m_ui.isotopeListWidget->currentRow();
  
    // If the item is already at top of list, do nothing.
    if (index == m_ui.isotopeListWidget->count() - 1)
      return;
  
    // Get the isotope itself from the atom.
    Isotope *isotope = atom->isotopeList().at(index);

    atom->removeIsotopeAt(index);
    atom->insertIsotopeAt(index + 1, isotope);
  
    QListWidgetItem *item = m_ui.isotopeListWidget->takeItem(index);
    m_ui.isotopeListWidget->insertItem(index + 1, item);
    m_ui.isotopeListWidget->setCurrentRow(index + 1);
    isotopeListWidgetItemSelectionChanged();

    setModified();
  }


  void 
  AtomDefDlg::applyAtomPushButtonClicked()
  {
    // We are asked to apply the data for the atom.

    // If no atom is selected, just return.

    QList<QListWidgetItem *> selectedList = 
      m_ui.atomListWidget->selectedItems();
  
    if (selectedList.size() != 1)
      return;

    // Get the index of the current atom item.
    int index = m_ui.atomListWidget->currentRow();

    Atom *atom = mp_list->at(index);
  
    // We do not want more than one atom by the same name or the same
    // symbol.

    QString editName = m_ui.nameLineEdit->text();

    // The syntax [A-Z][a-z]* is automatically validated using the
    // validator(see initialize()).
    QString editSymbol = m_ui.symbolLineEdit->text();
  
    // If an atom is found in the list with any of these two strings,
    // and that atom is not the one that is current in the atom list,
    // then we are making a double entry, which is not allowed.

    int nameRes = Atom::isNameInList(editName, *mp_list);
    if (nameRes != -1 && nameRes != index)
      {
      QMessageBox::warning(this, 
                        tr("massXpert - Atom definition"),
                        tr("An atom with same name exists already."),
                        QMessageBox::Ok);
      return;
      }
  
    int symbolRes = Atom::isSymbolInList(editSymbol, *mp_list);
    if (symbolRes != -1 && symbolRes != index)
      {
      QMessageBox::warning(this, 
                        tr("massXpert - Atom definition"),
                        tr("An atom with same symbol exists already."),
                        QMessageBox::Ok);
      return;
      }
  
    atom->setName(editName);
    atom->setSymbol(editSymbol);
  
    // Update the list widget item.

    QListWidgetItem *item = m_ui.atomListWidget->currentItem();
    item->setData(Qt::DisplayRole, atom->name());

    setModified();
  }


  void 
  AtomDefDlg::applyIsotopePushButtonClicked()
  {
    Application *application = static_cast<Application *>(qApp);
    QLocale locale = application->locale();

    // We are asked to apply the data for the isotope.

    // If no isotope is selected, just return.

    QList<QListWidgetItem *> selectedList = 
      m_ui.isotopeListWidget->selectedItems();
  
    if (selectedList.size() != 1)
      return;

    // Get the atom to which the isotope belongs. 
    int index = m_ui.atomListWidget->currentRow();
    Atom *atom = mp_list->at(index);

    // Get the index of the current isotope item.
    index = m_ui.isotopeListWidget->currentRow();
  
    // Get the isotope itself from the atom.
    Isotope *isotope = atom->isotopeList().at(index);
  
    QString editMass = m_ui.isotopeMassLineEdit->text();
    QString editAbundance = m_ui.isotopeAbundanceLineEdit->text();

    bool ok = false;
    double doubleMass = locale.toDouble(editMass, &ok);
  
    if (doubleMass == 0.0 && !ok)
      {
      QMessageBox::warning(this, 
                        tr("massXpert - Atom definition"),
                        tr("Failed to convert %1 to a double.")
                        .arg(editMass),
                        QMessageBox::Ok);
      return;
      }

    ok = false;
    double doubleAbundance = locale.toDouble(editAbundance, &ok);
  
    if (doubleAbundance == 0.0 && !ok)
      {
      QMessageBox::warning(this, 
                        tr("massXpert - Atom definition"),
                        tr("Failed to convert %1 to a double.")
                        .arg(editAbundance),
                        QMessageBox::Ok);
      return;
      }
  
    isotope->setMass(doubleMass);
    isotope->setAbundance(doubleAbundance);
  
    // Update the list widget item.

    QListWidgetItem *item = m_ui.isotopeListWidget->currentItem();
    QString mass = isotope->mass(locale, MXP_ATOM_DEC_PLACES);
    item->setData(Qt::DisplayRole, mass);

    atom->calculateMasses();

    updateAtomMassDetails(atom);

    setModified();
  }


  bool
  AtomDefDlg::validatePushButtonClicked()
  {
    QStringList errorList;
  
    // All we have to do is validate the atom definition. For that we'll
    // go in the listwidget items one after the other and make sure that
    // everything is fine and that colinearity is perfect between the
    // atom list and the listwidget.
  
    int itemCount = m_ui.atomListWidget->count();
  
    if (itemCount != mp_list->size())
      {
      errorList << QString(tr("\nThe number of atoms in in the list widget \n"
                          "and in the list of atoms is not identical.\n"));
      
      QMessageBox::warning(this, 
                        tr("massXpert - Atom definition"),
                        errorList.join("\n"),
                        QMessageBox::Ok);
      return false;
      }

    for (int iter = 0; iter < mp_list->size(); ++iter)
      {
      QListWidgetItem *item = m_ui.atomListWidget->item(iter);
      
      Atom *atom = mp_list->at(iter);
      
      if(item->text() != atom->name())
        errorList << QString(tr("\nAtom at index %1 has not the same\n"
                            "name as the list widget item at the\n"
                            "same index.\n")
                        .arg(iter));
      
      if(!atom->validate())
        errorList << QString(tr("\nAtom at index %1 failed to validate.\n")
                        .arg(iter));
      }

    if (errorList.size())
      {
      QMessageBox::warning(this, 
                        tr("massXpert - Atom definition"),
                        errorList.join("\n"),
                        QMessageBox::Ok);
      return false;
      }
    else
      {
      QMessageBox::warning(this, 
                        tr("massXpert - Atom definition"),
                       ("Validation: success\n"),
                        QMessageBox::Ok);
      }
  
    return true;
  }


  void 
  AtomDefDlg::atomListWidgetItemSelectionChanged()
  {
    Application *application = static_cast<Application *>(qApp);
    QLocale locale = application->locale();

    // The atom item has changed. Empty the isotope list and update its
    // contents. Update the details for the atom.

    // The list is a single-item-selection list.
  
    QList<QListWidgetItem *> selectedList = 
      m_ui.atomListWidget->selectedItems();
  
    if (selectedList.size() != 1)
      return;

    // Get the index of the current atom.
    int index = m_ui.atomListWidget->currentRow();
  
    Atom *atom = mp_list->at(index);
    Q_ASSERT(atom);
  
    // Set the data of the atom to their respective widgets.
    updateAtomIdentityDetails(atom);
    updateAtomMassDetails(atom);
  
    // The list of isotopes
    m_ui.isotopeListWidget->clear();
  
    for (int iter = 0; iter < atom->isotopeList().size(); ++iter)
      {
      Isotope *isotope = atom->isotopeList().at(iter);
      
      m_ui.isotopeListWidget->
        addItem(isotope->mass(locale,MXP_ATOM_DEC_PLACES));
      }

    if (!m_ui.isotopeListWidget->count())
      updateIsotopeDetails(0);
    else
      {
      // And now select the first row in the isotope list widget.
      m_ui.isotopeListWidget->setCurrentRow(0);
      }
  }


  void 
  AtomDefDlg::isotopeListWidgetItemSelectionChanged()
  {
    // The isotope item has changed. Update the details for the isotope.

    // The list is a single-item-selection list.
  
    QList<QListWidgetItem *> selectedList = 
      m_ui.isotopeListWidget->selectedItems();
  
    if (selectedList.size() != 1)
      return;

    // Get the index of the current atom.
    int index = m_ui.atomListWidget->currentRow();

    // Find the isotope object in the list of isotopes.
    Atom *atom = mp_list->at(index);
    Q_ASSERT(atom);

    // Get the index of the current isotope.
    index = m_ui.isotopeListWidget->currentRow();
  
    // Get the isotope that is currently selected from the atom's list
    // of isotopes.
    Isotope *isotope = atom->isotopeList().at(index);
    Q_ASSERT(isotope);
  
    // Set the data of the isotope to their respective widgets.
    updateIsotopeDetails(isotope);
  }


  void
  AtomDefDlg::updateAtomIdentityDetails(Atom *atom)
  {
    if (atom)
      {
      m_ui.nameLineEdit->setText(atom->name());
      m_ui.symbolLineEdit->setText(atom->symbol());
      }
    else
      {
      m_ui.nameLineEdit->setText("");
      m_ui.symbolLineEdit->setText("");
      } 
  }


  void
  AtomDefDlg::updateAtomMassDetails(Atom *atom)
  {
    Application *application = static_cast<Application *>(qApp);
    QLocale locale = application->locale();

    if (atom)
      {
      m_ui.monoMassLineEdit->
        setText(atom->mono(locale,MXP_ATOM_DEC_PLACES));
      m_ui.avgMassLineEdit->
        setText(atom->avg(locale,MXP_ATOM_DEC_PLACES));
      }
    else
      {
      m_ui.monoMassLineEdit->setText("");
      m_ui.avgMassLineEdit->setText("");
      } 
  }


  void
  AtomDefDlg::updateIsotopeDetails(Isotope *isotope)
  {
    Application *application = static_cast<Application *>(qApp);
    QLocale locale = application->locale();

    if (isotope)
      {
      m_ui.isotopeMassLineEdit->
        setText(isotope->mass(locale,MXP_ATOM_DEC_PLACES));
      m_ui.isotopeAbundanceLineEdit->
        setText(isotope->abundance(locale,MXP_ATOM_DEC_PLACES));
      }
    else
      {
      m_ui.isotopeMassLineEdit->setText("");
      m_ui.isotopeAbundanceLineEdit->setText("");
      }
  }


  void
  AtomDefDlg::clearAllDetails()
  {
    m_ui.nameLineEdit->setText("");
    m_ui.symbolLineEdit->setText("");
  
    m_ui.monoMassLineEdit->setText("");
    m_ui.avgMassLineEdit->setText("");
  
    m_ui.isotopeMassLineEdit->setText("");
    m_ui.isotopeAbundanceLineEdit->setText("");
  }


  void 
  AtomDefDlg::setModified()
  {
    mp_polChemDefWnd->setWindowModified(true); 
  }


  // VALIDATION
  bool
  AtomDefDlg::validate()
  {
    return validatePushButtonClicked();
  }

} // namespace massXpert

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