source: src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp@ 50246c

/*
 * 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 <boost/assign.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)
{
  qRegisterMetaType<atomId_t>("atomId_t");
  qRegisterMetaType<GLMoleculeObject_bond::SideOfBond>("GLMoleculeObject_bond::SideOfBond");

  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(insertMolecule(QtObservedMolecule::ptr)));
  connect(board, SIGNAL(moleculeRemoved(ObservedValue_Index_t)),
      this, SLOT(removeMolecule(ObservedValue_Index_t)));

  connect(board, SIGNAL(atomInserted(QtObservedAtom::ptr)),
      this, SLOT(connectAtom(QtObservedAtom::ptr)), Qt::DirectConnection);
  connect(this, SIGNAL(atomConnected(QtObservedAtom::ptr)),
      this, SLOT(insertAtom(QtObservedAtom::ptr)));
  connect(board, SIGNAL(atomRemoved(ObservedValue_Index_t)),
      this, SLOT(removeAtom(ObservedValue_Index_t)));

  connect(board, SIGNAL(bondInserted(QtObservedBond::ptr)),
      this, SLOT(connectBond(QtObservedBond::ptr)), Qt::DirectConnection);
  connect(this, SIGNAL(bondConnected(QtObservedBond::ptr)),
      this, SLOT(insertBond(QtObservedBond::ptr)));
  connect(board, SIGNAL(bondRemoved(ObservedValue_Index_t)),
      this, SLOT(removeBond(ObservedValue_Index_t)));

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

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

void GLWorldScene::clickAtom(atomId_t no)
{
   LOG(3, "INFO: GLWorldScene - atom " << no << " has been clicked.");
   const atom * const Walker = const_cast<const World &>(World::getInstance()).
       getAtom(AtomById(no));
   ASSERT( Walker != NULL,
       "GLWorldScene::clickAtom() - 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);
}

/** Prepares adding an atom to the scene
 *
 * We need to listen to moleculeChanged() in order to properly re-parent()
 * this QObject
 *
 * @param _atom atom to connect
 */
void GLWorldScene::connectAtom(QtObservedAtom::ptr _atom)
{
  connect(_atom.get(), SIGNAL(moleculeChanged()), this, SLOT(reparentAtom()));

  {
    const ObservedValue_Index_t atomid = _atom->getIndex();
    boost::recursive_mutex::scoped_lock lock(AtomNodeParentMap_mutex);
    AtomNodeParentMap[atomid] = static_cast<QObject *>(this);
  }

  emit atomConnected(_atom);
}

/** Adds an atom to the scene.
 *
 * @param _atom atom to add
 */
void GLWorldScene::insertAtom(QtObservedAtom::ptr _atom)
{
  LOG(3, "INFO: GLWorldScene: Received signal atomInserted for atom "
      << _atom->getAtomIndex());

  const ObservedValue_Index_t atomid = _atom->getIndex();
  QObject *parent = static_cast<QObject *>(this);
  GLMoleculeObject_atom *atomObject = NULL;
  {
    boost::recursive_mutex::scoped_lock lock(AtomNodeParentMap_mutex);
    AtomNodeParentMap_t::iterator parentiter = AtomNodeParentMap.find(atomid);
    if (parentiter != AtomNodeParentMap.end())
      parent = parentiter->second;
    else
      AtomNodeParentMap[atomid] = parent;

    atomObject = new GLMoleculeObject_atom(
            GLMoleculeObject::meshSphere,
            parent,
            _atom);
    ASSERT( atomObject != NULL,
        "GLWorldScene::atomInserted - could not create atom object for "
        +toString(_atom->getAtomIndex()));
  }
  AtomNodeMap::iterator iter = AtomsinSceneMap.find(atomid);
  ASSERT(iter == AtomsinSceneMap.end(),
      "GLWorldScene::insertAtom - same atom with id "
      +toString(_atom->getAtomIndex())+" added again.");
  AtomsinSceneMap.insert( make_pair(atomid, atomObject) );

  connect (atomObject, SIGNAL(clicked(atomId_t)), this, SLOT(clickAtom(atomId_t)));
  connect (atomObject, SIGNAL(changed()), this, SIGNAL(changed()));
  connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SIGNAL(changed()));
  connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SLOT(hoverChangedSignalled(GLMoleculeObject *)));

  emit changed();
  emit changeOccured();
}

/** Removes an atom.
 *
 * @param _atomid index of the atom that is removed
 */
void GLWorldScene::removeAtom(ObservedValue_Index_t _atomid)
{
  LOG(3, "INFO: GLWorldScene: Received signal atomRemoved for atom "+toString(_atomid)+".");
  // bonds are removed by signal coming from ~bond

  // remove atoms
  AtomNodeMap::iterator iter = AtomsinSceneMap.find(_atomid);
  ASSERT(iter != AtomsinSceneMap.end(),
      "GLWorldScene::removeAtom() - atom "+toString(_atomid)+" not on display.");
  GLMoleculeObject_atom *atomObject = iter->second;
  AtomsinSceneMap.erase(iter);
  delete atomObject;
  {
    boost::recursive_mutex::scoped_lock lock(AtomNodeParentMap_mutex);
    AtomNodeParentMap.erase(_atomid);
  }
  emit changed();
  emit changeOccured();
}

/** Prepares adding a bond to the scene
 *
 * We need to listen to moleculeChanged() in order to properly re-parent()
 * this QObject
 *
 * @param _bond bond to connect
 */
void GLWorldScene::connectBond(QtObservedBond::ptr _bond)
{
  connect(_bond.get(), SIGNAL(leftmoleculeChanged()), this, SLOT(reparentBondLeft()));
  connect(_bond.get(), SIGNAL(rightmoleculeChanged()), this, SLOT(reparentBondRight()));

  {
    const ObservedValue_Index_t bondid = _bond->getIndex();
    boost::recursive_mutex::scoped_lock lock(BondNodeParentMap_mutex);
    std::vector<QObject *> parents(2, static_cast<QObject *>(this));
    if ((_bond->getLeftAtom() != NULL) && (_bond->getLeftAtom()->getMoleculeRef() != NULL)) {
      const ObservedValue_Index_t molid = _bond->getLeftAtom()->getMoleculeRef()->getIndex();
      const MoleculeNodeMap::iterator leftiter = MoleculesinSceneMap.find(molid);
      if (leftiter != MoleculesinSceneMap.end())
        parents[0] = leftiter->second;
    }
    if ((_bond->getRightAtom() != NULL) && (_bond->getRightAtom()->getMoleculeRef() != NULL)) {
      const ObservedValue_Index_t molid = _bond->getRightAtom()->getMoleculeRef()->getIndex();
      const MoleculeNodeMap::iterator leftiter = MoleculesinSceneMap.find(molid);
      if (leftiter != MoleculesinSceneMap.end())
        parents[1] = leftiter->second;
    }
    BondNodeParentMap.insert( std::make_pair(bondid, parents) );
  }

  emit bondConnected(_bond);
}

/** Adds a bond to the scene.
 *
 * @param _bond bond to add
 */
void GLWorldScene::insertBond(QtObservedBond::ptr _bond)
{
  static const std::vector< GLMoleculeObject_bond::SideOfBond > bondsides =
      boost::assign::list_of<GLMoleculeObject_bond::SideOfBond>
          (GLMoleculeObject_bond::left)
          (GLMoleculeObject_bond::right);
  LOG(3, "INFO: GLWorldScene::insertBond() - Adding bonds " << _bond->getBondIndex());

  const ObservedValue_Index_t bondid = _bond->getIndex();
  std::vector<QObject *> parents(2, static_cast<QObject *>(this));
  {
    boost::recursive_mutex::scoped_lock lock(BondNodeParentMap_mutex);
    BondNodeParentMap_t::iterator parentiter = BondNodeParentMap.find(bondid);
    if (parentiter != BondNodeParentMap.end()) {
      parents = parentiter->second;
    } else
      BondNodeParentMap.insert( std::make_pair(bondid, parents) );

    BondNodeMap::iterator iter = BondsinSceneMap.find(bondid);
    ASSERT( iter == BondsinSceneMap.end(),
        "GLWorldScene::insertBond() - bond "+toString(bondid)+" is already known.");
    for (size_t i=0;i<2;++i) {
      GLMoleculeObject_bond *bondObject = new GLMoleculeObject_bond(
              GLMoleculeObject::meshCylinder,
              parents[i],
              _bond,
              bondsides[i]);
      connect (bondObject, SIGNAL(changed()), this, SIGNAL(changed()));
      BondsinSceneMap.insert( std::make_pair(bondid, bondObject) );
    }
  }

  emit changed();
  emit changeOccured();
}

/** Removes a bond.
 *
 * @param _bondid id of bond to remove
 */
void GLWorldScene::removeBond(ObservedValue_Index_t _bondid)
{
  LOG(3, "INFO: GLWorldScene::removedBond() - Removing bond to id " << _bondid);

  // left bond
  std::pair<BondNodeMap::iterator, BondNodeMap::iterator> iters =
      BondsinSceneMap.equal_range(_bondid);
  ASSERT( iters.first != iters.second,
      "GLWorldScene::removedBond() - could not find bond to id "+toString(_bondid));
  for (BondNodeMap::iterator iter = iters.first; iter != iters.second; ++iter) {
    GLMoleculeObject_bond *bondObject = iter->second;
    delete bondObject; // is done by signal from bond itself
    //LOG(4, "INFO: Still present bonds " << BondsinSceneMap << ".");
  }
  BondsinSceneMap.erase(_bondid);
  {
    boost::recursive_mutex::scoped_lock lock(BondNodeParentMap_mutex);
    BondNodeParentMap.erase(_bondid);
  }

  emit changed();
  emit changeOccured();
}

void GLWorldScene::hoverChangedSignalled(GLMoleculeObject *ob)
{
  // Find the atom, ob corresponds to.
  hoverAtomId = -1;
  GLMoleculeObject_atom *atomObject = dynamic_cast<GLMoleculeObject_atom *>(ob);
  if (atomObject){
    for (AtomNodeMap::iterator iter = AtomsinSceneMap.begin();iter != AtomsinSceneMap.end(); ++ iter){
      if (iter->second == atomObject)
        hoverAtomId = iter->second->objectId();
    }

    // Propagate signal.
    emit hoverChanged(hoverAtomId);
  } else {
    // Find the atom, ob corresponds to.
    GLMoleculeObject_molecule *moleculeObject = dynamic_cast<GLMoleculeObject_molecule *>(ob);
    if (moleculeObject){
      // Propagate signal.
      emit hoverChanged(moleculeObject->objectId(), 0);
    }
  }
}

void GLWorldScene::clickMolecule(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);
}

/** Inserts a molecule into the scene.
 *
 * @param _mol molecule to insert
 */
void GLWorldScene::insertMolecule(QtObservedMolecule::ptr _mol)
{
  const ObservedValue_Index_t molid = _mol->getIndex();
  LOG(3, "INFO: GLWorldScene: Received signal moleculeInserted for molecule "
      << _mol->getMolIndex());

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

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

  connect (molObject, SIGNAL(changed()), this, SIGNAL(changed()));
  connect (molObject, SIGNAL(changeOccured()), this, SIGNAL(changeOccured()));

  emit changed();
  emit changeOccured();
}

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

  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_molid);
  ASSERT ( iter != MoleculesinSceneMap.end(),
      "GLWorldScene::removeMolecule() - to be removed molecule "+toString(_molid)
      +" is already gone.");
  // check if it's already empty
  GLMoleculeObject_molecule *molObject = iter->second;
  delete molObject;
  MoleculesinSceneMap.erase(iter);

  emit changed();
  emit changeOccured();
}

void GLWorldScene::moleculesVisibilityChanged(ObservedValue_Index_t _id, bool _visible)
{
  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_id);
  ASSERT( iter != MoleculesinSceneMap.end(),
      "GLWorldScene::moleculeInserted() - molecule's id "
      +toString(board->getMoleculeIdToIndex(_id))+" is unknown.");

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

  emit changed();
  emit changeOccured();
}

/** Changes the parent of an object in the scene.
 *
 * \param _id index of the object whose parent to change
 * \param _ob new parent
 */
void GLWorldScene::reparentAtom()
{
  QtObservedAtom *walker = dynamic_cast<QtObservedAtom *>(sender());
  boost::recursive_mutex::scoped_lock lock(AtomNodeParentMap_mutex);
  const ObservedValue_Index_t walkerid = walker->getIndex();
  AtomNodeParentMap_t::iterator parentiter = AtomNodeParentMap.find(walkerid);
  ASSERT( parentiter != AtomNodeParentMap.end(),
      "GLWorldScene::reparentAtom() - could not find object to id "+toString(walkerid));
  AtomNodeMap::iterator atomiter = AtomsinSceneMap.find(walkerid);
  ASSERT( atomiter != AtomsinSceneMap.end(),
      "GLWorldScene::reparentAtom() - could not find GLMoleculeObject to id "+toString(walkerid));
  if (walker->getMoleculeRef() != NULL) {
    const ObservedValue_Index_t molid = walker->getMoleculeRef()->getIndex();
    MoleculeNodeMap::iterator moliter = MoleculesinSceneMap.find(molid);
    if (moliter != MoleculesinSceneMap.end()) {
      parentiter->second = moliter->second;
      atomiter->second->setParent(moliter->second);
    } else {
      // associated molecule has not yet been instantiated, keep in mind
      ASSERT(0,
          "GLWorldScene::reparentAtom() - new molecule not present yet?");
    }
  } else {
    parentiter->second = static_cast<QObject*>(this);
    atomiter->second->setParent(this);
  }
}

/** Changes the parent of an object in the scene.
 *
 * \param _id index of the object whose parent to change
 * \param _ob new parent
 */
void GLWorldScene::reparentBondLeft()
{
  QtObservedBond *bond = dynamic_cast<QtObservedBond *>(sender());
  boost::recursive_mutex::scoped_lock lock(BondNodeParentMap_mutex);
  const ObservedValue_Index_t bondid = bond->getIndex();
  BondNodeParentMap_t::iterator parentiter = BondNodeParentMap.find(bondid);
  ASSERT( parentiter != BondNodeParentMap.end(),
      "GLWorldScene::reparentBondLeft() - could not find object to id "+toString(bondid));
  BondNodeMap::iterator bonditer = BondsinSceneMap.find(bondid);
  ASSERT( bonditer != BondsinSceneMap.end(),
      "GLWorldScene::reparentBondLeft() - could not find GLMoleculeObject to id "+toString(bondid));
  if (bonditer->second->BondSide != GLMoleculeObject_bond::left)
    ++bonditer;
  ASSERT( (bonditer->first == bondid)
      && (bonditer->second->BondSide == GLMoleculeObject_bond::left),
      "GLWorldScene::reparentBondLeft() - could not find left-side bond.");
  if ((bond->getLeftAtom() != NULL) && (bond->getLeftAtom()->getMoleculeRef() != NULL)) {
    const ObservedValue_Index_t molid = bond->getLeftAtom()->getMoleculeRef()->getIndex();
    MoleculeNodeMap::iterator moliter = MoleculesinSceneMap.find(molid);
    if (moliter != MoleculesinSceneMap.end()) {
      parentiter->second[0] = moliter->second;
      bonditer->second->setParent(moliter->second);
    } else {
      // associated molecule has not yet been instantiated, keep in mind
      ASSERT(0,
          "GLWorldScene::reparentBondLeft() - new molecule not present yet?");
    }
  } else {
    parentiter->second[0] = static_cast<QObject*>(this);
    bonditer->second->setParent(this);
  }
}

/** Changes the parent of an object in the scene.
 *
 * \param _id index of the object whose parent to change
 * \param _ob new parent
 */
void GLWorldScene::reparentBondRight()
{
  QtObservedBond *bond = dynamic_cast<QtObservedBond *>(sender());
  boost::recursive_mutex::scoped_lock lock(BondNodeParentMap_mutex);
  const ObservedValue_Index_t bondid = bond->getIndex();
  BondNodeParentMap_t::iterator parentiter = BondNodeParentMap.find(bondid);
  ASSERT( parentiter != BondNodeParentMap.end(),
      "GLWorldScene::reparentBondLeft() - could not find object to id "+toString(bondid));
  BondNodeMap::iterator bonditer = BondsinSceneMap.find(bondid);
  ASSERT( bonditer != BondsinSceneMap.end(),
      "GLWorldScene::reparentBondLeft() - could not find GLMoleculeObject to id "+toString(bondid));
  if (bonditer->second->BondSide != GLMoleculeObject_bond::right)
    ++bonditer;
  ASSERT( (bonditer->first == bondid)
      && (bonditer->second->BondSide == GLMoleculeObject_bond::right),
      "GLWorldScene::reparentBondLeft() - could not find right-side bond.");
  if ((bond->getRightAtom() != NULL) && (bond->getRightAtom()->getMoleculeRef() != NULL)) {
    const ObservedValue_Index_t molid = bond->getRightAtom()->getMoleculeRef()->getIndex();
    MoleculeNodeMap::iterator moliter = MoleculesinSceneMap.find(molid);
    if (moliter != MoleculesinSceneMap.end()) {
      parentiter->second[1] = moliter->second;
      bonditer->second->setParent(moliter->second);
    } else {
      // associated molecule has not yet been instantiated, keep in mind
      ASSERT(0,
          "GLWorldScene::reparentBondRight() - new molecule not present yet?");
    }
  } else {
    parentiter->second[1] = static_cast<QObject*>(this);
    bonditer->second->setParent(this);
  }
}

/** 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);
}