source: src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp@ 8b59dd

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
 * Copyright (C)  2013 Frederik Heber. 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/>.
 */

/*
 * GLWorldScene.cpp
 *
 *  This is based on the Qt3D example "teaservice", specifically parts of teaservice.cpp.
 *
 *  Created on: Aug 17, 2011
 *      Author: heber
 */

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

#include "GLWorldScene.hpp"
#include <Qt3D/qglview.h>
#include <Qt3D/qglbuilder.h>
#include <Qt3D/qglscenenode.h>
#include <Qt3D/qglsphere.h>
#include <Qt3D/qglcylinder.h>

#include "UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp"
#include "UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp"
#include "UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp"
#include "UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp"
#include "UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.hpp"

#include "UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp"

#include "CodePatterns/MemDebug.hpp"

#include "CodePatterns/Log.hpp"

#include "Actions/SelectionAction/Atoms/AtomByIdAction.hpp"
#include "Actions/SelectionAction/Atoms/NotAtomByIdAction.hpp"
#include "Actions/SelectionAction/Molecules/MoleculeByIdAction.hpp"
#include "Actions/SelectionAction/Molecules/NotMoleculeByIdAction.hpp"
#include "Atom/atom.hpp"
#include "Bond/bond.hpp"
#include "Descriptors/AtomIdDescriptor.hpp"
#include "Descriptors/MoleculeIdDescriptor.hpp"
#include "Helpers/helpers.hpp"
#include "Shapes/ShapeRegistry.hpp"
#include "molecule.hpp"
#include "World.hpp"

#include <iostream>

using namespace MoleCuilder;

GLWorldScene::GLWorldScene(
    QtObservedInstanceBoard * _board,
    QObject *parent) :
  QObject(parent),
  selectionMode(SelectAtom),
  board(_board)
{
  int sphereDetails[] = {5, 3, 2, 0};
  int cylinderDetails[] = {16, 8, 6, 3};
  for (int i=0;i<GLMoleculeObject::DETAILTYPES_MAX;i++){
    QGLBuilder emptyBuilder;
    GLMoleculeObject::meshEmpty[i] = emptyBuilder.finalizedSceneNode();
    QGLBuilder sphereBuilder;
    sphereBuilder << QGLSphere(2.0, sphereDetails[i]);
    GLMoleculeObject::meshSphere[i] = sphereBuilder.finalizedSceneNode();
    GLMoleculeObject::meshSphere[i]->setOption(QGLSceneNode::CullBoundingBox, true);
    QGLBuilder cylinderBuilder;
    cylinderBuilder << QGLCylinder(.25,.25,1.0,cylinderDetails[i]);
    GLMoleculeObject::meshCylinder[i] = cylinderBuilder.finalizedSceneNode();
    GLMoleculeObject::meshCylinder[i]->setOption(QGLSceneNode::CullBoundingBox, true);
  }
  connect(board, SIGNAL(moleculeInserted(QtObservedMolecule::ptr)),
      this, SLOT(moleculeSignOn(QtObservedMolecule::ptr)), Qt::DirectConnection);
  connect(board, SIGNAL(moleculeRemoved(const moleculeId_t)),
      this, SLOT(moleculeSignOff(const moleculeId_t)), Qt::DirectConnection);
  connect(board, SIGNAL(moleculeIndexChanged(const moleculeId_t, const moleculeId_t)),
      this, SLOT(moleculeIndexChanged(const moleculeId_t, const moleculeId_t)));
  connect(board, SIGNAL(atomInserted(QtObservedAtom::ptr)),
      this, SLOT(atomInserted(QtObservedAtom::ptr)));
  connect(board, SIGNAL(atomRemoved(const atomId_t)),
      this, SLOT(atomRemoved(const atomId_t)));
  connect(this, SIGNAL(insertMolecule(QtObservedMolecule::ptr)),
      this, SLOT(moleculeInserted(QtObservedMolecule::ptr)) );
  connect(this, SIGNAL(removeMolecule(const moleculeId_t)),
      this, SLOT(moleculeRemoved(const moleculeId_t)) );

//  connect(this, SIGNAL(updated()), this, SLOT(update()));
}

GLWorldScene::~GLWorldScene()
{
  // remove all elements
  GLMoleculeObject::cleanMaterialMap();
}

void GLWorldScene::atomClicked(atomId_t no)
{
   LOG(3, "INFO: GLMoleculeObject_molecule - atom " << no << " has been clicked.");
   const atom * const Walker = const_cast<const World &>(World::getInstance()).
       getAtom(AtomById(no));
   ASSERT( Walker != NULL,
       "GLWorldScene::atomClicked() - clicked atom has disappeared.");
   if (selectionMode == SelectAtom){
     if (!World::getInstance().isSelected(Walker))
       SelectionAtomById(std::vector<atomId_t>(1,no));
     else
       SelectionNotAtomById(std::vector<atomId_t>(1,no));
   }else if (selectionMode == SelectMolecule){
     const molecule *mol = Walker->getMolecule();
     ASSERT(mol, "Atom without molecule has been clicked.");
     molids_t ids(1, mol->getId());
     if (!World::getInstance().isSelected(mol))
       SelectionMoleculeById(ids);
     else
       SelectionNotMoleculeById(ids);
   }
   emit clicked(no);
}

void GLWorldScene::moleculeClicked(moleculeId_t no)
{
   LOG(3, "INFO: GLMoleculeObject_molecule - mol " << no << " has been clicked.");
   const molecule * const mol= const_cast<const World &>(World::getInstance()).
       getMolecule(MoleculeById(no));
   ASSERT(mol, "Atom without molecule has been clicked.");
   molids_t ids(1, mol->getId());
   if (!World::getInstance().isSelected(mol))
     SelectionMoleculeById(ids);
   else
     SelectionNotMoleculeById(ids);
   emit clicked(no);
}

/** Prepares insertion of a general atom.
 *
 * This is called before the insertion into a molecule and thus before the
 * insertion into the scene.
 *
 * @param _atom atom to insert
 */
void GLWorldScene::atomInserted(QtObservedAtom::ptr _atom)
{
  const atomId_t atomid = _atom->getAtomIndex();
  ASSERT( QtObservedAtomMap.find(atomid) == QtObservedAtomMap.end(),
      "GLWorldScene::AtomInserted() - atom with id "+toString(atomid)
      +" is already present in QtObservedAtomMap.");
  QtObservedAtomMap[atomid] = _atom;
  connect(_atom.get(), SIGNAL(indexChanged(const atomId_t,const atomId_t)),
      this, SLOT(atomIndexChanged(const atomId_t,const atomId_t)) );
}

/** Removes an general atom.
 *
 * This is called when the atom has been removed from the molecule.
 *
 * @param _atom atom to remove
 */
void GLWorldScene::atomRemoved(const atomId_t _atomid)
{
  const QtObservedAtomMap_t::iterator eraseiter = QtObservedAtomMap.find(_atomid);
  ASSERT( eraseiter != QtObservedAtomMap.end(),
      "GLWorldScene::AtomRemoved() - atom with id "+toString(_atomid)
      +" is not present in QtObservedAtomMap.");
  disconnect(eraseiter->second.get(), SIGNAL(indexChanged(const atomId_t,const atomId_t)),
      this, SLOT(atomIndexChanged(const atomId_t,const atomId_t)) );
  QtObservedAtomMap.erase(eraseiter);
}

/** Inserts an atom into the scene when molecule is present.
 *
 * @param _atom atom to insert
 */
void GLWorldScene::moleculesAtomInserted(QtObservedAtom::ptr _atom, QtObservedMolecule * _mol)
{
  const atomId_t atomid = _atom->getAtomIndex();
  const atomId_t molid = _atom->getAtomMoleculeIndex();
  LOG(3, "INFO: GLWorldScene: Received signal atomInserted for atom "+toString(atomid)+".");

  // check of molecule is already present
  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
  const MoleculeNodeMap::iterator moliter = MoleculesinSceneMap.find(molid);
  if (moliter != MoleculesinSceneMap.end()) {
    // check that it is the right molecule
    QtObservedMolecule::ptr &checkmol = moliter->second->ObservedMolecule;
    if (checkmol.get() == _mol) {
      LOG(3, "INFO: GLWorldScene: Sending signal moleculesAtomInserted for atom "+toString(atomid)+".");
      QMetaObject::invokeMethod(moliter->second,        // pointer to a QObject
                                "atomInserted",       // member name (no parameters here)
                                Qt::QueuedConnection,     // connection type
                                Q_ARG(QtObservedAtom::ptr, _atom));     // parameters
    } else {
      // relay atomRemoved to GLMoleculeObject_molecule in RemovedMolecules
//      LOG(3, "INFO: GLWorldScene: Sending signal moleculesAtomInserted for atom "+toString(_atomid)
//          +" to molecule in RemovedMolecules.");
//      const MoleculeNodeMap::iterator removedmoliter = RemovedMolecules.find(molid);
//      ASSERT( removedmoliter != RemovedMolecules.end(),
//          "GLWorldScene::moleculesAtomInserted() - signal from old mol "
//          +toString(molid)+", but not present in RemovedMolecules");
//      QMetaObject::invokeMethod(removedmoliter->second,        // pointer to a QObject
//                                "atomInserted ",       // member name (no parameters here)
//                                Qt::QueuedConnection,     // connection type
//                                Q_ARG(QtObservedAtom::ptr, _atom));     // parameters
      ASSERT( 0,
          "GLWorldScene::moleculesAtomInserted() - would need to send atomInserted to already removed molecule.");
    }
  } else {
    boost::recursive_mutex::scoped_lock lock(MoleculeMissedStateMap_mutex);
    // only record missed state for molecule if (still) present but not instantiated
    if (QtObservedMoleculeMap.count(molid)) {
      // store signal for when it is instantiated
      if (MoleculeMissedStateMap.count(molid) == 0)
        MoleculeMissedStateMap.insert( std::make_pair(molid ,StateChangeMap_t()) );
      MoleculeMissedStateMap[molid].insert( std::make_pair(atomid, atomInsertedState) );
      ASSERT( QtObservedAtomMap[atomid] == _atom,
          "GLWorldScene::moleculesAtomInserted() - atom "+toString(atomid)
          +" inserted in molecule "+toString(molid)
          +" which does not match atom in QtObservedAtomMap.");
      LOG(3, "INFO: GLWorldScene: Placing atomInserted for atom " << atomid
           << " and molecule " << molid << " into missed state map.");
    }
  }
}

/** Removes an atom into the scene before molecule is present.
 *
 * @param _atomid atom to remove
 */
void GLWorldScene::moleculesAtomRemoved(const atomId_t _atomid, QtObservedMolecule * _mol)
{
  LOG(3, "INFO: GLWorldScene: Received signal atomRemoved for atom "+toString(_atomid)+".");

  // if atom is not in map, then GLMoleculeObject_molecule is already present anyway.
  if (QtObservedAtomMap.count(_atomid)) {
    const QtObservedAtom::ptr atom = QtObservedAtomMap[_atomid];
    const moleculeId_t molid = atom->getAtomMoleculeIndex();
    // check of molecule is already present
    boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
    const MoleculeNodeMap::iterator moliter = MoleculesinSceneMap.find(molid);
    if (moliter != MoleculesinSceneMap.end()) {
      QtObservedMolecule::ptr &checkmol = moliter->second->ObservedMolecule;
      if (checkmol.get() == _mol) {
        LOG(3, "INFO: GLWorldScene: Sending signal moleculesAtomRemoved for atom "+toString(_atomid)+".");
        QMetaObject::invokeMethod(moliter->second,        // pointer to a QObject
                                  "atomRemoved",       // member name (no parameters here)
                                  Qt::QueuedConnection,     // connection type
                                  Q_ARG(const atomId_t, _atomid));     // parameters
      } else {
        // relay atomRemoved to GLMoleculeObject_molecule in RemovedMolecules
        LOG(3, "INFO: GLWorldScene: Sending signal moleculesAtomRemoved for atom "+toString(_atomid)
            +" to molecule in RemovedMolecules.");
        const MoleculeNodeMap::iterator removedmoliter = RemovedMolecules.find(molid);
        ASSERT( removedmoliter != RemovedMolecules.end(),
            "GLWorldScene::moleculesAtomRemoved() - signal from old mol "
            +toString(molid)+", but not present in RemovedMolecules");
        QMetaObject::invokeMethod(removedmoliter->second,        // pointer to a QObject
                                  "atomRemoved",       // member name (no parameters here)
                                  Qt::QueuedConnection,     // connection type
                                  Q_ARG(const atomId_t, _atomid));     // parameters
      }
    } else {
      boost::recursive_mutex::scoped_lock lock(MoleculeMissedStateMap_mutex);
      // only record missed state for molecule if (still) present but not instantiated
      if (QtObservedMoleculeMap.count(molid)) {
        // store signal for when it is instantiated
        if (MoleculeMissedStateMap.count(molid) == 0)
          MoleculeMissedStateMap.insert( std::make_pair(molid, StateChangeMap_t()) );
        MoleculeMissedStateMap[molid].insert( std::make_pair(_atomid, atomRemovedState) );
        LOG(3, "INFO: GLWorldScene: Placing atomRemoved for atom " << _atomid
             << " and molecule " << molid << " into missed state map.");
      }
    }
  }
}

void GLWorldScene::moleculeSignOn(QtObservedMolecule::ptr _mol)
{
  // sign on to QtObservedMolecule to get atomInserted/..Removed signals from same
  // source as GLMoleculeObject_molecule would
  connect(_mol.get(), SIGNAL(atomInserted(QtObservedAtom::ptr, QtObservedMolecule *)),
      this, SLOT(moleculesAtomInserted(QtObservedAtom::ptr, QtObservedMolecule *)) );
  connect(_mol.get(), SIGNAL(atomRemoved(const atomId_t, QtObservedMolecule *)),
      this, SLOT(moleculesAtomRemoved(const atomId_t, QtObservedMolecule *)) );
  const moleculeId_t molid = _mol->getMolIndex();
  ASSERT( QtObservedMoleculeMap.find(molid) == QtObservedMoleculeMap.end(),
      "GLWorldScene::moleculeSignOn() - molecule with id "+toString(molid)
      +" is already present in QtObservedMoleculeMap.");
  QtObservedMoleculeMap[molid] = _mol;
  connect(_mol.get(), SIGNAL(indexChanged(const moleculeId_t,const moleculeId_t)),
      this, SLOT(moleculeIndexChanged(const moleculeId_t,const moleculeId_t)) );

  LOG(3, "INFO: GLWorldScene: Received signal moleculeSignOn for molecule "+toString(molid)+".");

  emit insertMolecule(_mol);
}

void GLWorldScene::moleculeSignOff(const moleculeId_t _id)
{
  const QtObservedMoleculeMap_t::iterator eraseiter = QtObservedMoleculeMap.find(_id);
  ASSERT( eraseiter != QtObservedMoleculeMap.end(),
      "GLWorldScene::moleculeSignOff() - cannot find id "+toString(_id)+" in map.");
  disconnect(eraseiter->second.get(), SIGNAL(indexChanged(const moleculeId_t,const moleculeId_t)),
      this, SLOT(moleculeIndexChanged(const moleculeId_t,const moleculeId_t)) );
  QtObservedMoleculeMap.erase(eraseiter);

  LOG(3, "INFO: GLWorldScene: Received signal moleculeSignOff for molecule "+toString(_id)+".");

  emit removeMolecule(_id);
}

/** Inserts a molecule into the scene.
 *
 * @param _mol molecule to insert
 */
void GLWorldScene::moleculeInserted(QtObservedMolecule::ptr _mol)
{
  ASSERT (_mol,
      "GLWorldScene::moleculeInserted() - received shared_ptr for molecule is empty?");
  const moleculeId_t molid = _mol->getMolIndex();
  LOG(3, "INFO: GLWorldScene: Received signal moleculeInserted for molecule "+toString(molid)+".");

  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);

  MoleculeNodeMap::const_iterator iter = MoleculesinSceneMap.find(molid);
  ASSERT( iter == MoleculesinSceneMap.end(),
      "GLWorldScene::moleculeInserted() - molecule's id "+toString(molid)+" already present.");

  // add new object
  LOG(1, "DEBUG: Adding GLMoleculeObject_molecule to id " << molid);
  GLMoleculeObject_molecule *molObject =
      new GLMoleculeObject_molecule(
          GLMoleculeObject::meshEmpty,
          this,
          *board,
          _mol);
  ASSERT( molObject != NULL,
      "GLWorldScene::moleculeInserted - could not create molecule object for "+toString(molid));
#ifndef NDEBUG
  std::pair<MoleculeNodeMap::iterator, bool> inserter =
#endif
  MoleculesinSceneMap.insert( make_pair(molid, molObject) );
  ASSERT(inserter.second,
      "GLWorldScene::moleculeInserted() - molecule "+toString(molid)+" already present in scene.");

  // now handle all state changes that came up before the instantiation
  if (MoleculeMissedStateMap.count(molid) != 0) {
//      ASSERT( !MoleculeMissedStateMap[molid].empty(),
//          "GLWorldScene::moleculeInserted() - we have an empty state change map for molecule with id "
//          +toString(molid));
    boost::recursive_mutex::scoped_lock lock(MoleculeMissedStateMap_mutex);
    for (StateChangeMap_t::iterator iter = MoleculeMissedStateMap[molid].begin();
        !MoleculeMissedStateMap[molid].empty();
        iter = MoleculeMissedStateMap[molid].begin()) {
      std::pair<StateChangeMap_t::iterator, StateChangeMap_t::iterator> rangeiter =
          MoleculeMissedStateMap[molid].equal_range(iter->first);
      const size_t StateCounts = std::distance(rangeiter.first, rangeiter.second);
      if (StateCounts > 1) {
        // more than one state change, have to combine
        typedef std::map<StateChangeType, size_t> StateChangeAmounts_t;
        StateChangeAmounts_t StateChangeAmounts;
        for (StateChangeMap_t::const_iterator stateiter = rangeiter.first;
            stateiter != rangeiter.second; ++stateiter)
          ++StateChangeAmounts[stateiter->second];
        ASSERT( StateChangeAmounts[atomInsertedState] >= StateChangeAmounts[atomRemovedState],
            "GLWorldScene::moleculeInserted() - more atomRemoved states "
            +toString(StateChangeAmounts[atomRemovedState])+" than atomInserted "
            +toString(StateChangeAmounts[atomInsertedState])+" for atom "+toString(iter->first));
        if (StateChangeAmounts[atomInsertedState] > StateChangeAmounts[atomRemovedState]) {
          LOG(1, "INFO: invoking atomInserted for atom " << iter->first);
          QMetaObject::invokeMethod(molObject,        // pointer to a QObject
                                    "atomInserted",       // member name (no parameters here)
                                    Qt::QueuedConnection,     // connection type
                                    Q_ARG(QtObservedAtom::ptr, QtObservedAtomMap[iter->first]));     // parameters
        } else {
          LOG(1, "INFO: Atom " << iter->first << " has been inserted and removed already.");
        }
        // removed all state changes for this atom
        MoleculeMissedStateMap[molid].erase(rangeiter.first, rangeiter.second);
      } else {
        // can only be an insertion
        switch (rangeiter.first->second) {
          case atomRemovedState:
            ASSERT( 0,
                "GLWorldScene::moleculeInserted() - atomRemoved state without atomInserted for atom "
                +toString(iter->first));
            break;
          case atomInsertedState:
          {
            LOG(1, "INFO: invoking atomInserted for atom " << iter->first);
            QMetaObject::invokeMethod(molObject,        // pointer to a QObject
                                      "atomInserted",       // member name (no parameters here)
                                      Qt::QueuedConnection,     // connection type
                                      Q_ARG(QtObservedAtom::ptr, QtObservedAtomMap[iter->first]));     // parameters
            break;
          }
          default:
            ASSERT( 0,
                "GLWorldScene::moleculeInserted() - there are unknown change states.");
            break;
        }
        // removed state changes for this atom
        MoleculeMissedStateMap[molid].erase(iter);
      }
    }
  }

  connect (molObject, SIGNAL(changed()), this, SIGNAL(changed()));
  connect (molObject, SIGNAL(changeOccured()), this, SIGNAL(changeOccured()));
  connect (molObject, SIGNAL(atomClicked(atomId_t)), this, SLOT(atomClicked(atomId_t)));
  connect (molObject, SIGNAL(moleculeClicked(moleculeId_t)), this, SLOT(moleculeClicked(moleculeId_t)));
  connect (molObject, SIGNAL(moleculeEmptied(moleculeId_t)), this, SLOT(moleculeEmpty(moleculeId_t)));
  connect (molObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
  connect (molObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
  connect (molObject, SIGNAL(hoverChanged(const atomId_t)), this, SIGNAL(hoverChanged(const atomId_t)));
  connect (molObject, SIGNAL(hoverChanged(const moleculeId_t, int)), this, SIGNAL(hoverChanged(const moleculeId_t, int)));
  connect (molObject, SIGNAL(hoverChanged(const moleculeId_t, int)), this, SIGNAL(hoverChanged(const moleculeId_t, int)));

  emit changed();
  emit changeOccured();

  // remove state change map for the molecule
  {
    boost::recursive_mutex::scoped_lock lock(MoleculeMissedStateMap_mutex);
    MoleculeMissedStateMap.erase(molid);
  }
}

/** Removes a molecule from the scene.
 *
 * @param _id id of molecule to remove
 */
void GLWorldScene::moleculeRemoved(const moleculeId_t _id)
{
  LOG(3, "INFO: GLWorldScene: Received signal moleculeRemoved for molecule "+toString(_id)+".");

  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);

  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_id);
  if ( iter != MoleculesinSceneMap.end()) {
    LOG(1, "DEBUG: Removing GLMoleculeObject_molecule to id " << _id << " from scene.");
    RemovedMolecules.insert( std::make_pair(_id, iter->second) );
    MoleculesinSceneMap.erase(iter);
  }

  // remove any possible state changes left
  {
    boost::recursive_mutex::scoped_lock lock(MoleculeMissedStateMap_mutex);
    MoleculeMissedStateMap.erase(_id);
  }
}

void GLWorldScene::moleculeEmpty(const moleculeId_t _id)
{
  LOG(3, "INFO: GLWorldScene: Received signal moleculeEmpty for molecule "+toString(_id)+".");

  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);

  MoleculeNodeMap::iterator iter = RemovedMolecules.find(_id);
  if ( iter != RemovedMolecules.end()) {
    LOG(1, "DEBUG: Deleting GLMoleculeObject_molecule to id " << _id);
    GLMoleculeObject_molecule *molObject = iter->second;
    RemovedMolecules.erase(iter);
    molObject->disconnect();
    delete molObject;
  } else {
    ASSERT(0,
        "GLWorldScene::moleculeEmpty() - molecule "+toString(_id)+" is empty that is not present.");
  }

  // remove any possible state changes left
  {
    boost::recursive_mutex::scoped_lock lock(MoleculeMissedStateMap_mutex);
    MoleculeMissedStateMap.erase(_id);
  }

  emit changed();
  emit changeOccured();
}

void GLWorldScene::atomIndexChanged(const atomId_t _oldid, const atomId_t _newid)
{
  if (QtObservedAtomMap.count(_oldid)) {
    const QtObservedAtom::ptr atom = QtObservedAtomMap[_oldid];
    QtObservedAtomMap.erase(_oldid);
    QtObservedAtomMap.insert( std::make_pair(_newid, atom) );
  }
}

void GLWorldScene::moleculeIndexChanged(const moleculeId_t _oldid, const moleculeId_t _newid)
{
  {
    QtObservedMoleculeMap_t::iterator const olditer = QtObservedMoleculeMap.find(_oldid);
    ASSERT ( olditer != QtObservedMoleculeMap.end(),
        "GLWorldScene::moleculeIndexChanged() - molecule "
        +toString(_oldid)+" not present in QtObservedMoleculeMap.");
#ifndef NDEBUG
    QtObservedMoleculeMap_t::iterator const newiter = QtObservedMoleculeMap.find(_newid);
    ASSERT ( newiter == QtObservedMoleculeMap.end(),
        "GLWorldScene::moleculeIndexChanged() - molecule "
        +toString(_newid)+" already present in QtObservedMoleculeMap.");
#endif
    const QtObservedMolecule::ptr mol = olditer->second;
    QtObservedMoleculeMap.erase(olditer);
    QtObservedMoleculeMap[_newid] = mol;
  }
  {
    MoleculeNodeMap::iterator const olditer = MoleculesinSceneMap.find(_oldid);
    if ( olditer != MoleculesinSceneMap.end()) {
#ifndef NDEBUG
      MoleculeNodeMap::iterator const newiter = MoleculesinSceneMap.find(_newid);
      ASSERT ( newiter == MoleculesinSceneMap.end(),
          "GLWorldScene::moleculeIndexChanged() - molecule "
          +toString(_newid)+" already present in MoleculesinSceneMap.");
#endif
      LOG(1, "DEBUG: Changing GLMoleculeObject_molecule in MoleculesinSceneMapfrom "
          << _oldid << " to id " << _newid);
      GLMoleculeObject_molecule* const molObject = olditer->second;
      MoleculesinSceneMap.erase(olditer);
      MoleculesinSceneMap[_newid] = molObject;
    }
  }
  {
    MoleculeNodeMap::iterator const olditer = RemovedMolecules.find(_oldid);
    if ( olditer != RemovedMolecules.end()) {
#ifndef NDEBUG
      MoleculeNodeMap::iterator const newiter = RemovedMolecules.find(_newid);
      ASSERT ( newiter == RemovedMolecules.end(),
          "GLWorldScene::moleculeIndexChanged() - molecule "
          +toString(_newid)+" already present in RemovedMolecules.");
#endif
      LOG(1, "DEBUG: Changing GLMoleculeObject_molecule in RemovedMolecules from "
          << _oldid << " to id " << _newid);
      GLMoleculeObject_molecule* const molObject = olditer->second;
      RemovedMolecules.erase(olditer);
      RemovedMolecules[_newid] = molObject;
    }
  }
}

void GLWorldScene::moleculesVisibilityChanged(const moleculeId_t _id, bool _visible)
{
  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);
  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_id);
  ASSERT( iter != MoleculesinSceneMap.end(),
      "GLWorldScene::moleculeInserted() - molecule's id "+toString(_id)+" is unknown.");

  GLMoleculeObject_molecule *molObject = iter->second;
  molObject->setVisible(_visible);

  emit changed();
  emit changeOccured();
}

/** Adds a shape to the scene.
 *
 */
void GLWorldScene::addShape(const std::string &_name)
{
  Shape * const shape = ShapeRegistry::getInstance().getByName(_name);
  if (shape != NULL) {
    GLMoleculeObject_shape *shapeObject = new GLMoleculeObject_shape(*shape, this);
    ShapeNodeMap::iterator iter = ShapesinSceneMap.find(_name);
    ASSERT(iter == ShapesinSceneMap.end(),
        "GLWorldScene::addShape() - same shape "+_name+" added again.");
    ShapesinSceneMap.insert( make_pair(_name, shapeObject) );
  } else
    ELOG(2, "GLWorldScene::addShape() - shape disappeared before we could draw it.");

  emit changed();
}

void GLWorldScene::removeShape(const std::string &_name)
{
  ShapeNodeMap::iterator iter = ShapesinSceneMap.find(_name);
  ASSERT(iter != ShapesinSceneMap.end(),
      "GLWorldScene::removeShape() - shape "+_name+" not in scene.");
  ShapesinSceneMap.erase(iter);
  delete(iter->second);

  emit changed();
}

void GLWorldScene::updateSelectedShapes()
{
  foreach (QObject *obj, children()) {
    GLMoleculeObject_shape *shapeobj = qobject_cast<GLMoleculeObject_shape *>(obj);
      if (shapeobj){
        shapeobj->enable(ShapeRegistry::getInstance().isSelected(shapeobj->getShape()));
      }
  }

  emit changed();
}

void GLWorldScene::initialize(QGLView *view, QGLPainter *painter) const
{
  // Initialize all of the mesh objects that we have as children.
   foreach (QObject *obj, children()) {
     GLMoleculeObject *meshobj = qobject_cast<GLMoleculeObject *>(obj);
       if (meshobj)
         meshobj->initialize(view, painter);
   }
}

void GLWorldScene::draw(QGLPainter *painter, const QVector4D &cameraPlane) const
{
   // Draw all of the mesh objects that we have as children.
   foreach (QObject *obj, children()) {
     GLMoleculeObject *meshobj = qobject_cast<GLMoleculeObject *>(obj);
       if (meshobj)
         meshobj->draw(painter, cameraPlane);
   }
}

void GLWorldScene::setSelectionMode(SelectionModeType mode)
{
  selectionMode = mode;
  // TODO send update to toolbar
}

void GLWorldScene::setSelectionModeAtom()
{
  setSelectionMode(SelectAtom);
}

void GLWorldScene::setSelectionModeMolecule()
{
  setSelectionMode(SelectMolecule);
}