source: src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp@ a39d72

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
 * 
 *
 *   This file is part of MoleCuilder.
 *
 *    MoleCuilder 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 2 of the License, or
 *    (at your option) any later version.
 *
 *    MoleCuilder 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 MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 * QtMoleculeList.cpp
 *
 *  Created on: Jan 21, 2010
 *      Author: crueger
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "QtMoleculeList.hpp"

#include <QModelIndex>
#include <QDebug>

#include "UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp"
#include "UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.hpp"

#include <boost/bind.hpp>
#include <boost/thread/locks.hpp>
#include <iostream>

#include "CodePatterns/MemDebug.hpp"

#include "CodePatterns/Log.hpp"
#include "CodePatterns/Observer/Notification.hpp"

#include "Atom/atom.hpp"
#include "Descriptors/MoleculeIdDescriptor.hpp"
#include "Formula.hpp"
#include "molecule.hpp"
#include "MoleculeListClass.hpp"

using namespace std;

const unsigned int QtMoleculeList::update_times_per_second = 20;

QtMoleculeList::QtMoleculeList() :
  Observer("QtMoleculeList"),
  ChangingChildrensVisibility(false),
  update_timer(NULL),
  callback_DirtyItems(boost::bind(&QtMoleculeList::informDirtyState, this, _1, _2, _3)),
  callback_subjectKilledItems(boost::bind(&QtMoleculeList::receiveSubjectKilled, this, _1))
{
  setColumnCount(QtMoleculeItemFactory::COLUMNCOUNT);

  World::getInstance().signOn(this, World::MoleculeInserted);

  refill();

//  qRegisterMetaType<QItemSelection>("QItemSelection");
  //connect(this,SIGNAL(cellChanged(int,int)),this,SLOT(moleculeChanged(int,int)));
//  connect(selectionModel(),SIGNAL(selectionChanged(QItemSelection, QItemSelection)),this,SLOT(rowsSelected(QItemSelection, QItemSelection)));
  connect(this, SIGNAL(itemChanged(QStandardItem*)), this, SLOT(checkForVisibilityChange(QStandardItem*)), Qt::DirectConnection);
}

QtMoleculeList::~QtMoleculeList()
{
  World::getInstance().signOff(this, World::MoleculeInserted);
}

QVariant QtMoleculeList::headerData(int section, Qt::Orientation orientation, int role) const
{
  if (role == Qt::DisplayRole) {
    if (orientation == Qt::Horizontal) {
      if (section < QtMoleculeItem::COLUMNTYPES_MAX)
        return QString(QtMoleculeItemFactory::COLUMNNAMES[section]);
    }
  }
  return QVariant();
}

void QtMoleculeList::update(Observable *publisher) {
  ASSERT(0,
      "QtMoleculeList::update() - we did not sign up for any global updates.");
}

bool QtMoleculeList::isMoleculeItemPresent(const moleculeId_t _molid) const
{
  boost::recursive_mutex::scoped_lock lock(map_mutex);
  MoleculeItemBiMap_t::left_const_iterator iter =
      MoleculeItemBiMap.left.find(_molid);
  return ( iter != MoleculeItemBiMap.left.end());
}

QtMoleculeItem * QtMoleculeList::MoleculeIdToItem(const moleculeId_t _molid) const
{
  boost::recursive_mutex::scoped_lock lock(map_mutex);
  MoleculeItemBiMap_t::left_const_iterator iter =
      MoleculeItemBiMap.left.find(_molid);
  ASSERT( iter != MoleculeItemBiMap.left.end(),
      "QtMoleculeList::MoleculeIdToItem() - could not find item to id "
      +toString(_molid));
  return iter->second;
}

const moleculeId_t QtMoleculeList::ItemToMoleculeId(const QtMoleculeItem * const _item) const
{
  boost::recursive_mutex::scoped_lock lock(map_mutex);
  const MoleculeItemBiMap_t::right_const_iterator iter =
      MoleculeItemBiMap.right.find(const_cast<QtMoleculeItem * const>(_item));
  if (iter != MoleculeItemBiMap.right.end())
    return iter->second;
  else
    return -1;
}

QtMoleculeItem * QtMoleculeList::getSpecificMoleculeItem(
    const QtMoleculeItem * const _item,
    const enum QtMoleculeItem::COLUMNTYPES _type) const
{
  QStandardItem *parent_item = _item->parent();
  ASSERT( parent_item != NULL,
      "QtMoleculeList::getSpecificMoleculeItem() - parent of molecule item is NULL");
  return static_cast<QtMoleculeItem *>(parent_item->child(_item->index().row(), _type));
}

bool QtMoleculeList::isGroupItemPresent(const std::string &_formula) const
{
  boost::recursive_mutex::scoped_lock lock(map_mutex);
  FormulaTreeItemBiMap_t::left_const_iterator iter =
      FormulaItemBiMap.left.find(_formula);
  return ( iter != FormulaItemBiMap.left.end());
}

QStandardItem * QtMoleculeList::FormulaToGroupItem(const std::string &_formula) const
{
  boost::recursive_mutex::scoped_lock lock(map_mutex);
  FormulaTreeItemBiMap_t::left_const_iterator iter =
      FormulaItemBiMap.left.find(_formula);
  ASSERT( iter != FormulaItemBiMap.left.end(),
      "QtMoleculeList::FormulaToGroupItem() - could not find item to formula "
      +toString(_formula));
  return iter->second;
}

const std::string& QtMoleculeList::GroupItemToFormula(const QStandardItem * const _item) const
{
  boost::recursive_mutex::scoped_lock lock(map_mutex);
  static std::string emptystring;
  const FormulaTreeItemBiMap_t::right_const_iterator iter =
      FormulaItemBiMap.right.find(const_cast<QStandardItem * const>(_item));
  if (iter != FormulaItemBiMap.right.end())
    return iter->second;
  else
    return emptystring;
}

QStandardItem * QtMoleculeList::getSpecificGroupItem(
    const QStandardItem * const _item,
    const enum QtMoleculeItem::COLUMNTYPES _type) const
{
  return invisibleRootItem()->child(_item->index().row(), _type);
}

const QModelIndex QtMoleculeList::MoleculeIdToIndex(const moleculeId_t _id) const
{
  boost::recursive_mutex::scoped_lock lock(refill_mutex);
  QtMoleculeItem * const item = MoleculeIdToItem(_id);
  ASSERT(item != NULL,
      "QtMoleculeList::MoleculeIdToIndex() - could not find item to "
      +toString(_id));
  return indexFromItem(item);
}

const moleculeId_t QtMoleculeList::IndexToMoleculeId(const QModelIndex &_index) const
{
  boost::recursive_mutex::scoped_lock lock(refill_mutex);
  QtMoleculeItem * const item = dynamic_cast<QtMoleculeItem *>(itemFromIndex(_index));
  if (item == NULL)
    return -1;
  else
    return ItemToMoleculeId(item);
}

void QtMoleculeList::receiveSubjectKilled(const moleculeId_t _id)
{
  boost::recursive_mutex::scoped_lock lock(map_mutex);
  KilledItemsPerMolecule_t::iterator iter = KilledItemsPerMolecule.find(_id);
  if (iter == KilledItemsPerMolecule.end())
    KilledItemsPerMolecule.insert( std::make_pair(_id, 1));
  else
    ++(iter->second);
  if (iter->second == QtMoleculeItem::COLUMNTYPES_MAX) {
    boost::recursive_mutex::scoped_lock lock(listAccessing_mutex);
    removedMolecules.push_back( _id );
  }
}

void QtMoleculeList::recieveNotification(Observable *publisher, Notification_ptr notification)
{
  if (dynamic_cast<World *>(publisher) != NULL) {
    switch (notification->getChannelNo()) {
      case World::MoleculeInserted:
      {
        boost::recursive_mutex::scoped_lock lock(listAccessing_mutex);
        const moleculeId_t molid = const_cast<const World &>(World::getInstance()).lastChangedMolId();
        if (molid != (unsigned int )-1)
          newMolecules.push_back( molid );
        break;
      }
      default:
        ASSERT(0, "QtMoleculeList::recieveNotification() - cannot get here, not subscribed to channel "
            +toString(notification->getChannelNo()));
        break;
    }
  }
}

void QtMoleculeList::addGroupItem(
    QStandardItem *&mainitem,
    const std::string &_molecule_formula)
{
  QList<QStandardItem *> groupItems =
      QtMoleculeItemFactory::getInstance().createGroupItems(_molecule_formula);
  mainitem = groupItems.front();
  {
    boost::recursive_mutex::scoped_lock lock(map_mutex);
    FormulaItemBiMap.left.insert( std::make_pair(_molecule_formula, mainitem) );
  }
  invisibleRootItem()->appendRow(groupItems);
}

QList<QStandardItem *> QtMoleculeList::createMoleculeItems(
    const moleculeId_t _molid,
    std::string &_molecule_formula)
{
  QList<QStandardItem *> molItems =
      QtMoleculeItemFactory::getInstance().createMoleculeItems(
          _molid,
          callback_DirtyItems,
          callback_subjectKilledItems);
  QtMoleculeItem *mol_item = dynamic_cast<QtMoleculeItem *>(molItems.front());
  ASSERT( mol_item != NULL,
      "QtMoleculeList::createMoleculeItems() - item from factory was not a QtMoleculeItem?");
  {
    boost::recursive_mutex::scoped_lock lock(map_mutex);
    MoleculeItemBiMap.left.insert( std::make_pair(_molid, mol_item) );
  }

  QStandardItem *formulaitem = molItems.at(QtMoleculeItem::FORMULA);
  ASSERT( formulaitem != NULL,
      "QtMoleculeList::createMoleculeItems() - Formula item not created by factory?");
  _molecule_formula = formulaitem->text().toStdString();
  {
    boost::recursive_mutex::scoped_lock lock(map_mutex);
    LOG(1, "Adding " << _molecule_formula << " for " << _molid << " to MoleculeFormulaMap.");
    MoleculeFormulaMap.insert( std::make_pair( _molid, _molecule_formula) );
  }
//  LOG(1, "Inserting molecule " << _mol->getId() << ": " << _mol);
  return molItems;
}

std::string QtMoleculeList::addMolecule(const molecule * const _mol)
{
  // find group if already in list
  QStandardItem *groupItem = NULL;

  // create molecule items and obtain the molecule's formula
  std::string molecule_formula;
  QList<QStandardItem *> molItems = createMoleculeItems(_mol->getId(), molecule_formula);

  // new molecule type -> create new group
  if (!isGroupItemPresent(molecule_formula)){
    // insert new formula entry into visibility
#ifndef NDEBUG
    std::pair< FormulaVisibilityCountMap_t::iterator, bool> visibilityinserter =
#endif
        FormulaVisibilityCountMap.insert(
            std::make_pair( molecule_formula, (unsigned int)0) );
    ASSERT( visibilityinserter.second,
        "QtMoleculeList::refill() - molecule with formula "
        +molecule_formula+" already in FormulaVisibilityCountMap.");

    // create item and place into Map with formula as key
    addGroupItem(groupItem, molecule_formula);
  } else {
    groupItem = FormulaToGroupItem(molecule_formula);
  }
  ASSERT( groupItem != NULL,
      "QtMoleculeList::addMolecule() - item with id "+toString(_mol->getId())
      +" has no parent?");
  groupItem->appendRow(molItems);

  return molecule_formula;
}

void QtMoleculeList::removeMoleculeItem(QtMoleculeItem * const _item)
{
  boost::recursive_mutex::scoped_lock lock(refill_mutex);
  const QModelIndex mol_index = indexFromItem(_item);
  QStandardItem *groupitem = _item->parent();
  const QModelIndex group_index = groupitem->index();
  {
    boost::recursive_mutex::scoped_lock lock(map_mutex);
    MoleculeItemBiMap_t::right_iterator removeiter =
        MoleculeItemBiMap.right.find(_item);
    ASSERT( removeiter != MoleculeItemBiMap.right.end(),
        "QtMoleculeList::removeMoleculeItem() - could not find item in MoleculeBiMap.");
  //  LOG(1, "Erasing molecule " << (removeiter->second));
    {
      MoleculeFormulaMap_t::iterator removeformulaiter =
          MoleculeFormulaMap.find(removeiter->second);
      ASSERT( removeformulaiter != MoleculeFormulaMap.end(),
          "QtMoleculeList::removeMoleculeItem() - could not find id "
          +toString(removeiter->second)+" in MoleculeFormulaMap.");
      LOG(1, "Removing " << removeformulaiter->second << " for "
          << removeformulaiter->first << " from MoleculeFormulaMap.");
      MoleculeFormulaMap.erase( removeformulaiter );
    }
    MoleculeItemBiMap.right.erase(removeiter);
  }
  removeRows(mol_index.row(), 1, group_index);
}

void QtMoleculeList::refill()
{
  // check timer's presence
  if (update_timer == NULL) {
    update_timer = new QTimer(this);
    connect( update_timer, SIGNAL(timeout()), this, SLOT(checkState()));
  } else
    update_timer->stop();

  {
    boost::recursive_mutex::scoped_lock refill_lock(refill_mutex);
    boost::recursive_mutex::scoped_lock listAccessing_lock(listAccessing_mutex);

    //  LOG(1, "Clearing list.");

    clear();
    FormulaVisibilityCountMap.clear();
    {
      boost::recursive_mutex::scoped_lock lock(map_mutex);
      FormulaItemBiMap.clear();
      MoleculeFormulaMap.clear();
      MoleculeItemBiMap.clear();
      KilledItemsPerMolecule.clear();
    }
    dirtyMolItems.clear();
    visibilityMolItems.clear();
    visibilityGroupItems.clear();
    newMolecules.clear();
    removedMolecules.clear();
    toBeMovedItems.clear();
  }

  const std::vector<const molecule*> &molecules =
      const_cast<const World &>(World::getInstance()).getAllMolecules();
  for (std::vector<const molecule*>::const_iterator iter = molecules.begin();
      iter != molecules.end();
      iter++)
    addMolecule(*iter);

  // activate timer
  update_timer->start(1000/update_times_per_second);
}

bool QtMoleculeList::areAnyItemsDirty()
{
  // get whether any items are dirty
  boost::recursive_mutex::scoped_lock lock(listAccessing_mutex);
  bool dirty = false;
  dirty |= !dirtyMolItems.empty();
  dirty |= !visibilityMolItems.empty();
  dirty |= !dirtyGroupItems.empty();
  dirty |= !visibilityGroupItems.empty();
  dirty |= !newMolecules.empty();
  dirty |= !removedMolecules.empty();
  dirty |= !toBeMovedItems.empty();
  return dirty;
}

void QtMoleculeList::checkState()
{
  const bool dirty = areAnyItemsDirty();
  // update if required
  if (dirty)
    updateItemStates();
}

void QtMoleculeList::subjectKilled(Observable *publisher)
{}

void QtMoleculeList::checkForVisibilityChange(QStandardItem* _item)
{
//  qDebug() << "Item changed called.";

  boost::recursive_mutex::scoped_lock lock(refill_mutex);
  if (_item->index().column() == QtMoleculeItem::VISIBILITY) {
//    qDebug() << "visibilityItem changed: " << (_item->checkState() ? "checked" : "unchecked");
    boost::recursive_mutex::scoped_lock lock(listAccessing_mutex);
    if ((_item->parent() == NULL) || (_item->parent() == invisibleRootItem()))
      visibilityGroupItems.insert( std::make_pair(
          GroupItemToFormula(_item->parent()), QtMoleculeItem::VISIBILITY) );
    else
      visibilityMolItems.insert(
          static_cast<QtMoleculeItem *>(_item)->getMoleculeId()
          );
  }
}

void QtMoleculeList::setVisibilityForMoleculeItem(QtMoleculeItem* _item)
{
  if (ChangingChildrensVisibility)
    return;

  boost::recursive_mutex::scoped_lock lock(refill_mutex);
  const bool visible = _item->checkState();
  const moleculeId_t molid = _item->getMoleculeId();
  std::string molecule_formula("illegal");
  {
    boost::recursive_mutex::scoped_lock lock(map_mutex);
    MoleculeFormulaMap_t::const_iterator formulaiter =
        MoleculeFormulaMap.find(molid);
    ASSERT( formulaiter != MoleculeFormulaMap.end(),
        "QtMoleculeList::setVisibilityForMoleculeItem() - formula of molecule "
        +toString(molid)+" unknown.");
    molecule_formula = formulaiter->second;
  }
  ASSERT( FormulaVisibilityCountMap.count(molecule_formula) != 0,
        "QtMoleculeList::setVisibilityForMoleculeItem() - molecule with formula " +molecule_formula
        +" is not present in FormulaVisibilityCountMap.");

  // get parent
  QStandardItem *groupItem = _item->parent();
  QStandardItem *visgroupItem = getSpecificGroupItem(groupItem, QtMoleculeItem::VISIBILITY);
  ASSERT( groupItem != NULL,
      "QtMoleculeList::setVisibilityForMoleculeItem() - item with id "
      +toString(_item->getMoleculeId())+" has not parent?");
  // check whether we have to set the group item

  ChangingChildrensVisibility = true;
  if (visible) {
    ++(FormulaVisibilityCountMap[molecule_formula]);
    // compare with occurence/total number of molecules
    if (FormulaVisibilityCountMap[molecule_formula] ==
        (unsigned int)(groupItem->rowCount()))
      visgroupItem->setCheckState(Qt::Checked);
  } else {
    --(FormulaVisibilityCountMap[molecule_formula]);
    // none selected anymore?
    if (FormulaVisibilityCountMap[molecule_formula] == 0)
      visgroupItem->setCheckState(Qt::Unchecked);
  }
  ChangingChildrensVisibility = false;

  emit moleculesVisibilityChanged(_item->getMolecule()->getId(), visible);
}

void QtMoleculeList::setVisibilityForGroupItem(QStandardItem* _item)
{
  if (ChangingChildrensVisibility)
    return;

  ChangingChildrensVisibility = true;

  boost::recursive_mutex::scoped_lock lock(refill_mutex);
  // go through all children, but don't enter for groupItem once more
  const bool visible = _item->checkState();
  QStandardItem *groupitem = getSpecificGroupItem(_item, QtMoleculeItem::NAME);
  for (int i=0;i<groupitem->rowCount();++i) {
    QtMoleculeItem *molItem = dynamic_cast<QtMoleculeItem *>(
        groupitem->child(i, QtMoleculeItem::VISIBILITY));
    if (molItem->checkState() != visible) {
      molItem->setCheckState(visible ? Qt::Checked : Qt::Unchecked);

      // emit signal
      emit moleculesVisibilityChanged(molItem->getMolecule()->getId(), visible);
    }
  }
  // set current number of visible children
  const std::string molecule_formula =
      GroupItemToFormula( getSpecificGroupItem(_item, QtMoleculeItem::NAME) );
  FormulaVisibilityCountMap_t::iterator countiter =
      FormulaVisibilityCountMap.find(molecule_formula);
  ASSERT( countiter != FormulaVisibilityCountMap.end(),
      "QtMoleculeList::setVisibilityForGroupItem() - molecules "+molecule_formula
      +" have no entry in visibility count map?");
  countiter->second = visible ? groupitem->rowCount() : 0;

  ChangingChildrensVisibility = false;
}


void QtMoleculeList::moleculeChanged() {
  /*int idx = verticalHeaderItem(row)->data(Qt::UserRole).toInt();
  molecule *mol = molecules->ReturnIndex(idx);
  string cellValue = item(row,QtMoleculeItem::NAME)->text().toStdString();
  if(mol->getName() != cellValue && cellValue !="") {
    mol->setName(cellValue);
  }
  else if(cellValue==""){
    item(row,QtMoleculeItem::NAME)->setText(QString(mol->getName().c_str()));
  }*/
}


int QtMoleculeList::setOccurrence(QStandardItem * const _groupitem)
{
  boost::recursive_mutex::scoped_lock lock(refill_mutex);
  QModelIndex modelindex = _groupitem->index();
  ASSERT( modelindex.isValid(),
      "QtMoleculeList::setOccurrence() - groupitem not associated to model anymore.");
  const int index = modelindex.row();
  QStandardItem *parent_item =
      _groupitem->parent() == NULL ? invisibleRootItem() : _groupitem->parent();
  ASSERT( parent_item != NULL,
      "QtMoleculeList::setOccurrence() - group item at "+toString(index)
      +" does not have a parent?");
  QStandardItem *occ_item = parent_item->child(index, QtMoleculeItem::OCCURRENCE);
  ASSERT( occ_item != NULL,
      "QtMoleculeList::setOccurrence() - group item at "+toString(index)
      +" does not have an occurrence?");
  const int count = _groupitem->rowCount();
  if (count == 0) {
    // we have to remove the group item completely
    boost::recursive_mutex::scoped_lock lock(map_mutex);
    const std::string molecule_formula = _groupitem->text().toStdString();
    FormulaItemBiMap.left.erase(molecule_formula);
    FormulaVisibilityCountMap.erase(molecule_formula);
    return index;
  } else {
    occ_item->setText(QString::number(count));
    return -1;
  }
}

std::string QtMoleculeList::readdItem(QtMoleculeItem *_molitem)
{
  boost::recursive_mutex::scoped_lock lock(refill_mutex);
  // use takeRows of molecule ..
  QStandardItem *groupitem = _molitem->parent();
  ASSERT( groupitem != NULL,
      "QtMoleculeList::readdItem() - mol item at "+toString(_molitem->index().row())
      +" does not have a groupitem?");
  // get updated formula from the item
  QStandardItem *formulaitem =
      _molitem->parent()->child(_molitem->index().row(), QtMoleculeItem::FORMULA);
  const std::string molecule_formula = formulaitem->text().toStdString();
  QList<QStandardItem *> mol_row = _molitem->parent()->takeRow(_molitem->index().row());
  // ..  and re-add where new formula fits
  if (!isGroupItemPresent(molecule_formula)) {
    // add new group item and formula entry
     addGroupItem(groupitem, molecule_formula);
  } else {
    groupitem = FormulaToGroupItem(molecule_formula);
  }
  ASSERT( groupitem != NULL,
      "QtMoleculeList::readdItem() - failed to create a sensible new groupitem");
  // finally add again
  groupitem->appendRow(mol_row);

  return molecule_formula;
}

void QtMoleculeList::informDirtyState(
    const moleculeId_t _id,
    const QtMoleculeItem::COLUMNTYPES _type,
    const QtMoleculeItem::MoveTypes _movetype)
{
  listAccessing_mutex.lock();
  dirtyMolItems.insert( std::make_pair(_id, _type) );
  listAccessing_mutex.unlock();

  if (_movetype == QtMoleculeItem::NeedsMove) {
    // we have to convert whatever item raised the dirty signal to the first
    // item in the row as otherwise multiple items in the row are selected
    // as to be moved, i.e. the same row is moved multiple times
    listAccessing_mutex.lock();
    toBeMovedItems.insert(_id);
    listAccessing_mutex.unlock();
  }
}

void QtMoleculeList::updateItemStates()
{
  /// copy lists such that new signals for dirty/.. may come in right away
  // TODO: if we had move semantics ...
  listAccessing_mutex.lock();
  list_of_molecule_items_t dirtyMolItems_copy = dirtyMolItems;
  dirtyMolItems.clear();
  list_of_molecules_t visibilityMolItems_copy = visibilityMolItems;
  visibilityMolItems.clear();
  list_of_group_items_t dirtyGroupItems_copy = dirtyGroupItems;
  dirtyGroupItems.clear();
  list_of_group_items_t visibilityGroupItems_copy = visibilityGroupItems;
  visibilityGroupItems.clear();
  std::vector<moleculeId_t> newMolecules_copy = newMolecules;
  newMolecules.clear();
  std::vector<moleculeId_t> removedMolecules_copy = removedMolecules;
  removedMolecules.clear();
  list_of_molecules_t toBeMovedItems_copy = toBeMovedItems;
  toBeMovedItems.clear();
  listAccessing_mutex.unlock();

  // wait till initial refill has been executed
  boost::recursive_mutex::scoped_lock lock(refill_mutex);

//  LOG(1, "Starting update.");

  // remove removedMolecules from other lists.
  for (std::vector<moleculeId_t>::const_iterator removeiter = removedMolecules_copy.begin();
      removeiter != removedMolecules_copy.end(); ++removeiter) {
    for (unsigned int i=0;i< QtMoleculeItem::COLUMNTYPES_MAX; ++i)
        dirtyMolItems_copy.erase( std::make_pair(*removeiter,(QtMoleculeItem::COLUMNTYPES)i) );
    toBeMovedItems_copy.erase(*removeiter);
    visibilityMolItems_copy.erase(*removeiter);
  }

  /// 1a. do the update for each dirty item
  for (list_of_molecule_items_t::const_iterator dirtyiter = dirtyMolItems_copy.begin();
      dirtyiter != dirtyMolItems_copy.end(); ++dirtyiter) {
    if (!isMoleculeItemPresent(dirtyiter->first))
      continue;
    QtMoleculeItem * const mol_item =
        getSpecificMoleculeItem(
            MoleculeIdToItem(dirtyiter->first),
            dirtyiter->second);
//    LOG(1, "Updating item " << mol_item);
    mol_item->updateState();
  }

  /// 1b. do the visibility update for each dirty item
  for (list_of_molecules_t::const_iterator visiter = visibilityMolItems_copy.begin();
      visiter != visibilityMolItems_copy.end(); ++visiter) {
    if (!isMoleculeItemPresent(*visiter))
      continue;
    QtMoleculeItem * const visitem =
      getSpecificMoleculeItem(
          MoleculeIdToItem(*visiter),
          QtMoleculeItem::VISIBILITY );
//    LOG(1, "Updating visibility of item " << visitem);
    setVisibilityForMoleculeItem(visitem);
  }

  /// 2. move all items that need to be moved
  typedef std::set<std::string> formulas_t;
  formulas_t toBeSetOccurrence;
  for (list_of_molecules_t::const_iterator moveiter = toBeMovedItems_copy.begin();
      moveiter != toBeMovedItems_copy.end(); ++moveiter) {
    boost::recursive_mutex::scoped_lock lock(map_mutex);
//    LOG(1, "Moving item " << molitem);
    MoleculeFormulaMap_t::iterator formulaiter =
        MoleculeFormulaMap.find(*moveiter);
    ASSERT( formulaiter != MoleculeFormulaMap.end(),
        "QtMoleculeList::updateItemStates() - formula of molecule "
        +toString(*moveiter)+" unknown.");
//    LOG(1, "Adding " << formulaiter->second << " to toBeSetOccurrence.");
    toBeSetOccurrence.insert( formulaiter->second );
    if (!isMoleculeItemPresent(*moveiter))
      continue;
    QtMoleculeItem *const molitem = MoleculeIdToItem(*moveiter);
    LOG(1, "Moving item " << molitem);
    const molecule *mol = molitem->getMolecule();
    if (mol != NULL) {
      // remove from formula<->molecule bimap with old formula
      LOG(1, "Removing " << formulaiter->second << " for " << formulaiter->first << " from MoleculeFormulaMap.");
      MoleculeFormulaMap.erase( formulaiter );
      const std::string formula = readdItem(molitem);
      // and add to formula<->molecule bimap with updated formula
      LOG(1, "Adding " << formula << " for " << *moveiter << " to MoleculeFormulaMap.");
      MoleculeFormulaMap.insert( std::make_pair(*moveiter, formula) );
//      LOG(1, "Adding " << formula << " to toBeSetOccurrence.");
      toBeSetOccurrence.insert( formula );
    }
  }

  /// 3. remove all items whose molecules have been removed
  for (std::vector<moleculeId_t>::const_iterator removeiter = removedMolecules_copy.begin();
      removeiter != removedMolecules_copy.end(); ++removeiter) {
//    LOG(1, "Removing molecule " << *removeiter);
    if (!isMoleculeItemPresent(*removeiter))
      continue;
    QtMoleculeItem *item = MoleculeIdToItem(*removeiter);
    if (item != NULL) {
      const std::string formula = item->parent()->text().toStdString();
//      LOG(1, "Adding " << formula << " to toBeSetOccurrence.");
      toBeSetOccurrence.insert( formula );
      removeMoleculeItem(item);
      KilledItemsPerMolecule.erase( *removeiter );
    }
  }

  // throw out items that we added by an update() while we are in this function
  listAccessing_mutex.lock();
  for (std::vector<moleculeId_t>::const_iterator removeiter = removedMolecules_copy.begin();
      removeiter != removedMolecules_copy.end(); ++removeiter) {
    for (unsigned int i=0;i< QtMoleculeItem::COLUMNTYPES_MAX; ++i)
        dirtyMolItems.erase( std::make_pair(*removeiter,(QtMoleculeItem::COLUMNTYPES)i) );
    toBeMovedItems.erase(*removeiter);
    visibilityMolItems.erase(*removeiter);
  }
  listAccessing_mutex.unlock();
  // after that it is not a problem as items have been removed (hence signOff() was called)

  /// 4. instantiate all new items
  for (std::vector<moleculeId_t>::const_iterator moliter = newMolecules_copy.begin();
      moliter != newMolecules_copy.end(); ++moliter) {
//    LOG(1, "Adding molecule " << *moliter);
    // check that World knows the molecule still
    const molecule * const mol = const_cast<const World &>(World::getInstance()).
        getMolecule(MoleculeById(*moliter));
    if ((mol != NULL) && (mol->getId() == *moliter)) {
      const std::string formula = addMolecule(mol);;
//      LOG(1, "Adding " << formula << " to toBeSetOccurrence.");
      toBeSetOccurrence.insert( formula );
    } else {
      ELOG(2, "Molecule " << *moliter
          << " disappeared before we could render it in QtMoleculeList.");
    }
  }

  /// 5a. update the group item's occurrence and visibility
  std::set<int> RowsToRemove;
  for (std::set<std::string>::const_iterator groupiter = toBeSetOccurrence.begin();
      groupiter != toBeSetOccurrence.end(); ++groupiter) {
//    LOG(1, "Updating group item's occurence " << *groupiter);
    QStandardItem *groupitem = FormulaToGroupItem(*groupiter);
    const int index = setOccurrence(groupitem);
    if (index != -1) {
//      LOG(1, "Removing row of group item " << groupitem);
      RowsToRemove.insert(index);
    }
  }
  toBeSetOccurrence.clear();

  // remove all visibility updates whose row is removed
  for (list_of_group_items_t::iterator visiter = visibilityGroupItems_copy.begin();
      visiter != visibilityGroupItems_copy.end(); ) {
      QStandardItem * const groupitem = FormulaToGroupItem(visiter->first);
    if (RowsToRemove.count(groupitem->index().row()) != 0) {
//      LOG(1, "Removing vis item " << *visiter << " because of removed group item.");
      visibilityGroupItems_copy.erase(visiter++);
    } else
      ++visiter;
  }

  // update visibility of all group items
  for (list_of_group_items_t::iterator visiter = visibilityGroupItems_copy.begin();
      visiter != visibilityGroupItems_copy.end(); ++visiter) {
//    LOG(1, "Updating visibility of item " << *visiter);
    QStandardItem * const groupitem =
        getSpecificGroupItem(FormulaToGroupItem(visiter->first),
        visiter->second);
    setVisibilityForGroupItem(groupitem);
  }

  /// 5b. remove all rows with 0 occurrence starting from last
  for (std::set<int>::reverse_iterator riter = RowsToRemove.rbegin();
      riter != RowsToRemove.rend(); ++riter) {
//    LOG(1, "Removing group item at row " << *riter);
    removeRows(*riter, 1, invisibleRootItem()->index());
  }

  // and done
//  LOG(1, "Done with update.");
}