Changeset 65c323

Timestamp:

Feb 12, 2016, 11:15:23 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

494478

Parents:

41e287

git-author:

Frederik Heber <heber@…> (10/29/15 10:46:45)

git-committer:

Frederik Heber <heber@…> (02/12/16 23:15:23)

Message:

Extracted all ObservedValue functionality out of GLMoleculeObject_atom.

• i.e. GLMoleculeObject_atom is reduced to simple displaying, updated via Qt signals. These signals are connected to a QtObservedAtom which in turn now contains all the ObservedValue functionality.
• this is preparatory for having a single (Observed)Atom as representer of its associated World's atom in the QtGui part of the code.

Location:

src/UIElements

Files:

• Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) (2 diffs)
• Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) (2 diffs)
• Qt4/InstanceBoard/QtObservedAtom.cpp (modified) (1 diff)
• Qt4/InstanceBoard/QtObservedAtom.hpp (modified) (6 diffs)
• Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) (4 diffs)
• Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) (2 diffs)
• Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) (8 diffs)
• Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) (4 diffs)
• Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) (1 diff)

src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp

@@ -33 +33 @@
    *
    * \param _name name used in debugging and prints
+   * \param _board ref to InstanceBoard
    */
-  ObservedValuesContainer(const std::string _name) :
-    NameOfType(_name)
-  {}
-
-  /** Dstor of class ObservedValuesContainer.
-   *
-   */
-  ~ObservedValuesContainer()
-  {}
+  ObservedValuesContainer(
+      const std::string _name,
+      QtObservedInstanceBoard &_board);
 
   /** Delivers the set of Observed value for the instance identified by \a _id.
@@ -69 +64 @@
   //!> name used in describing the instance type
   const std::string NameOfType;
+
+  //!> reference to InstanceBoard for callbacks on subjectKilled()
+  QtObservedInstanceBoard &board;
 
 private:

src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp

@@ -20 +20 @@
 
 template <class T, typename id>
+ObservedValuesContainer<T,id>::ObservedValuesContainer(
+    const std::string _name,
+    QtObservedInstanceBoard &_board) :
+  NameOfType(_name),
+  board(_board)
+{}
+
+template <class T, typename id>
 typename T::ptr ObservedValuesContainer<T,id>::get(const id _id)
 {
@@ -29 +37 @@
   // increase refcount
   ++(iter->second.second);
-  typename T::ptr _molecule(new T(obsvalues));
+  typename T::ptr _molecule(new T(obsvalues, board));
+
+  return _molecule;
+}
+
+template <>
+typename QtObservedMolecule::ptr
+ObservedValuesContainer<QtObservedMolecule,moleculeId_t>::get(const moleculeId_t _id)
+{
+  typename CountedObservedValues_t::iterator iter = ObservedValues.find(_id);
+  ASSERT( iter != ObservedValues.end(),
+      "ObservedValuesContainer::getObservedValues() - no observed values present for "
+      +NameOfType+" "+toString(_id));
+  const ObservedValues_t &obsvalues = iter->second.first;
+  // increase refcount
+  ++(iter->second.second);
+  typename QtObservedMolecule::ptr _molecule(new QtObservedMolecule(obsvalues));
 
   return _molecule;

src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp

@@ -36 +36 @@
 #include "QtObservedAtom.hpp"
 
+#include "UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp"
+
 #include "CodePatterns/MemDebug.hpp"
 
+#include <boost/assign.hpp>
+
+#include "Atom/atom.hpp"
+#include "Bond/bond.hpp"
+#include "Descriptors/AtomIdDescriptor.hpp"
+#include "Element/element.hpp"
+#include "World.hpp"
+
+#include "UIElements/Views/Qt4/Qt3D/ObservedValue_wCallback.hpp"
+
+using namespace boost::assign;
+
+static const Observable::channels_t getAtomBondsChannels()
+{
+  Observable::channels_t channels;
+  channels += AtomObservable::BondsAdded, AtomObservable::BondsRemoved;
+  return channels;
+}
+
+static const Observable::channels_t getAllObservedChannels()
+{
+  Observable::channels_t channels;
+  channels +=
+      AtomObservable::IndexChanged,
+      AtomObservable::PositionChanged,
+      AtomObservable::ElementChanged,
+      AtomObservable::BondsAdded,
+      AtomObservable::BondsRemoved;
+  return channels;
+}
+
+// static entities
+const Observable::channels_t
+QtObservedAtom::AtomIndexChannels(1, AtomObservable::IndexChanged);
+const Observable::channels_t
+QtObservedAtom::AtomPositionChannels(1, AtomObservable::PositionChanged);
+const Observable::channels_t
+QtObservedAtom::AtomElementChannels(1, AtomObservable::ElementChanged);
+const Observable::channels_t
+QtObservedAtom::AtomBondsChannels(getAtomBondsChannels());
+
 QtObservedAtom::QtObservedAtom(
-    const ObservedValues_t &_obsvalues,
+    const ObservedValues_t &_ObservedValues,
+    QtObservedInstanceBoard &_board,
     QWidget * _parent) :
   QWidget(_parent),
   Observer("QtObservedAtom"),
-  obsvalues(_obsvalues)
-{}
+  subjectKilledCount(0),
+  AllsignedOnChannels(getAllObservedChannels().size()),
+  signedOffChannels(0),
+  owner(NULL),
+  board(_board),
+  ObservedValues(_ObservedValues)
+{
+  activateObserver();
+}
 
 QtObservedAtom::~QtObservedAtom()
-{}
+{
+  deactivateObserver();
+}
+
+const atom * const QtObservedAtom::getAtomConst(const atomId_t _id)
+{
+  const atom * const _atom = const_cast<const World &>(World::getInstance()).
+      getAtom(AtomById(_id));
+  return _atom;
+}
+
+atom * const QtObservedAtom::getAtom(const atomId_t _id)
+{
+  atom * const _atom = World::getInstance().getAtom(AtomById(_id));
+  return _atom;
+}
+
+atomId_t QtObservedAtom::updateIndex()
+{
+  return const_cast<const World &>(World::getInstance()).lastChangedAtomId();
+}
+
+Vector QtObservedAtom::updatePosition(
+    const boost::function<const atomId_t ()> &_getAtomIndex)
+{
+  const atom * const _atom = getAtomConst(_getAtomIndex());
+  if (_atom != NULL) {
+    return _atom->getPosition();
+  } else {
+    return zeroVec;
+  }
+}
+
+atomicNumber_t QtObservedAtom::updateElement(
+    const boost::function<const atomId_t ()> &_getAtomIndex)
+{
+  const atom * const _atom = getAtomConst(_getAtomIndex());
+  if (_atom != NULL) {
+    return _atom->getElementNo();
+  } else {
+    return (atomicNumber_t)-1;
+  }
+}
+
+QtObservedAtom::ListOfBonds_t QtObservedAtom::updateBonds(
+    const boost::function<const atomId_t ()> &_getAtomIndex)
+{
+  ListOfBonds_t ListOfBonds;
+  const atom * const _atom = getAtomConst(_getAtomIndex());
+  if (_atom != NULL) {
+    // make sure bonds is up-to-date
+    const BondList ListBonds = _atom->getListOfBonds();
+    for (BondList::const_iterator iter = ListBonds.begin();
+        iter != ListBonds.end();
+        ++iter)
+      ListOfBonds.insert( ListOfBonds.end(), std::make_pair(
+          (*iter)->leftatom->getId(),
+          (*iter)->rightatom->getId()) );
+  }
+  return ListOfBonds;
+}
 
 void QtObservedAtom::update(Observable *publisher)
-{}
+{
+  ASSERT(0, "QtObservedAtom::update() - we are not signed on for global updates.");
+}
 
 void QtObservedAtom::subjectKilled(Observable *publisher)
-{}
+{
+  ++signedOffChannels;
+
+  if (signedOffChannels == AllsignedOnChannels) {
+    // remove owner: no more signOff needed
+    owner = NULL;
+
+    board.atomcountsubjectKilled(getAtomIndex());
+  }
+}
 
 void QtObservedAtom::recieveNotification(Observable *publisher, Notification_ptr notification)
-{}
+{
+  // ObservedValues have been updated before, hence convert updates to Qt's signals
+  switch (notification->getChannelNo()) {
+    case AtomObservable::IndexChanged:
+      emit indexChanged();
+      break;
+    case AtomObservable::PositionChanged:
+      emit positionChanged();
+      break;
+    case AtomObservable::ElementChanged:
+      emit elementChanged();
+      break;
+    case AtomObservable::BondsAdded:
+    case AtomObservable::BondsRemoved:
+      emit bondsChanged();
+      break;
+    default:
+      ASSERT(0, "QtObservedAtom::recieveNotification() - we are not signed on to channel "
+          +toString(notification->getChannelNo())+" of the atom.");
+      break;
+  }
+}
+
+void QtObservedAtom::activateObserver()
+{
+  atom * atomref = getAtom(getAtomIndex());
+  if (atomref != NULL) {
+    Observable::channels_t channels = getAllObservedChannels();
+    owner = static_cast<const Observable *>(atomref);
+    for (Observable::channels_t::const_iterator iter = channels.begin();
+        iter != channels.end(); ++iter)
+      owner->signOn(this, *iter);
+  } else
+    signedOffChannels = getAllObservedChannels().size();
+}
+
+void QtObservedAtom::deactivateObserver()
+{
+  // sign Off
+  if (owner != NULL) {
+    Observable::channels_t channels = getAllObservedChannels();
+    for (Observable::channels_t::const_iterator iter = channels.begin();
+        iter != channels.end(); ++iter)
+      owner->signOff(this, *iter);
+    owner = NULL;
+    signedOffChannels = AllsignedOnChannels;
+  }
+}
+
+void QtObservedAtom::initObservedValues(
+    ObservedValues_t &_ObservedValues,
+    const atomId_t _id,
+    const atom * const _atomref,
+    const boost::function<void(const atomId_t)> &_subjectKilled)
+{
+  /* This is an old note from when the code was still part of cstor's initializer body.
+   * TODO: Probably does not apply anymore but has not yet been tested.
+   *
+   * We must not use boost::cref(this) as "this" has not been properly constructed and seemingly
+   * boost::cref tries to do some magic to grasp the inheritance hierarchy which fails because
+   * the class has not been fully constructed yet. "This" itself seems to be working fine.
+   */
+
+  ASSERT( _ObservedValues.size() == MAX_ObservedTypes,
+      "QtObservedAtom::initObservedValues() - given ObservedValues has not correct size.");
+
+  // fill ObservedValues: index first
+  const boost::function<atomId_t ()> AtomIndexUpdater(
+      boost::bind(&QtObservedAtom::updateIndex));
+
+  ObservedValue_wCallback<atomId_t> * const IndexObservable =
+      new ObservedValue_wCallback<atomId_t>(
+          _atomref,
+          boost::bind(&QtObservedAtom::updateIndex),
+          "AtomIndex_"+toString(_id),
+          _id,
+          AtomIndexChannels,
+          _subjectKilled);
+  _ObservedValues[AtomIndex] = IndexObservable;
+
+  const boost::function<const atomId_t ()> AtomIndexGetter =
+      boost::bind(&ObservedValue_wCallback<atomId_t>::get,
+          IndexObservable);
+
+  // fill ObservedValues: then all the other that need index
+  const boost::function<Vector ()> AtomPositionUpdater(
+      boost::bind(&QtObservedAtom::updatePosition, AtomIndexGetter));
+  const boost::function<atomicNumber_t ()> AtomElementUpdater(
+      boost::bind(&QtObservedAtom::updateElement, AtomIndexGetter));
+  const boost::function<ListOfBonds_t ()> AtomBondsUpdater(
+      boost::bind(&QtObservedAtom::updateBonds, AtomIndexGetter));
+
+  _ObservedValues[AtomPosition] = new ObservedValue_wCallback<Vector, atomId_t>(
+      _atomref,
+      AtomPositionUpdater,
+      "AtomPosition_"+toString(_id),
+      AtomPositionUpdater(),
+      AtomPositionChannels,
+      _subjectKilled,
+      AtomIndexGetter);
+  _ObservedValues[AtomElement] = new ObservedValue_wCallback<atomicNumber_t, atomId_t>(
+      _atomref,
+      AtomElementUpdater,
+      "AtomElement"+toString(_id),
+      AtomElementUpdater(),
+      AtomElementChannels,
+      _subjectKilled,
+      AtomIndexGetter);
+  _ObservedValues[AtomBonds] = new ObservedValue_wCallback<ListOfBonds_t, atomId_t>(
+      _atomref,
+      AtomBondsUpdater,
+      "AtomBonds_"+toString(_id),
+      AtomBondsUpdater(),
+      AtomBondsChannels,
+      _subjectKilled,
+      AtomIndexGetter);
+}
+
+void QtObservedAtom::destroyObservedValues(
+    std::vector<boost::any> &_ObservedValues)
+{
+  delete boost::any_cast<ObservedValue_wCallback<atomId_t> *>(_ObservedValues[AtomIndex]);
+  delete boost::any_cast<ObservedValue_wCallback<Vector, atomId_t> *>(_ObservedValues[AtomPosition]);
+  delete boost::any_cast<ObservedValue_wCallback<atomicNumber_t, atomId_t> *>(_ObservedValues[AtomElement]);
+  delete boost::any_cast<ObservedValue_wCallback<ListOfBonds_t, atomId_t> *>(_ObservedValues[AtomBonds]);
+  _ObservedValues.clear();
+}
+
+atomId_t QtObservedAtom::getAtomIndex() const
+{
+  return boost::any_cast<ObservedValue_wCallback<atomId_t> *>(ObservedValues[AtomIndex])->get();
+}
+
+Vector QtObservedAtom::getAtomPosition() const
+{
+  return boost::any_cast<ObservedValue_wCallback<Vector, atomId_t> *>(ObservedValues[AtomPosition])->get();
+}
+
+atomicNumber_t QtObservedAtom::getAtomElement() const
+{
+  return boost::any_cast<ObservedValue_wCallback<atomicNumber_t, atomId_t> *>(ObservedValues[AtomElement])->get();
+}
+
+QtObservedAtom::ListOfBonds_t QtObservedAtom::getAtomBonds() const
+{
+  return boost::any_cast<ObservedValue_wCallback<ListOfBonds_t, atomId_t> *>(ObservedValues[AtomBonds])->get();
+}

src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp

@@ -17 +17 @@
 #include <QtGui/QWidget>
 
-
+#include <boost/function.hpp>
 #include <boost/shared_ptr.hpp>
 
+#include "CodePatterns/Observer/Observable.hpp"
 #include "CodePatterns/Observer/Observer.hpp"
+
+#include "LinearAlgebra/Vector.hpp"
 
 #include "UIElements/Qt4/InstanceBoard/ObservedValue_types.hpp"
@@ -26 +29 @@
 #include "types.hpp"
 
+class atom;
 class QtObservedInstanceBoard;
 
@@ -37 +41 @@
  *
  * This is the instance for information about a particular atom.
+ *
+ * Essentially, this is the interface between molecuilder's World (and a
+ * particular atom) and the QtGui part of the code.
  */
 class QtObservedAtom : public QWidget, public Observer
@@ -42 +49 @@
   Q_OBJECT
 
+public:
+
+  //!> typedef for instance wrapped in shared ptr
+  typedef boost::shared_ptr<QtObservedAtom> ptr;
+
+private:
   //!> ObservedValuesContainer needs to access private cstor and dstor
   friend class ObservedValuesContainer<QtObservedAtom, atomId_t>;
@@ -47 +60 @@
   friend class QtObservedInstanceBoard;
 
-  //!> typedef for instance wrapped in shared ptr
-  typedef boost::shared_ptr<QtObservedAtom> ptr;
-
   /** Cstor of QtObservedAtom.
    *
-   * \param _obsvalues ref to set of observed values for this instance
+   * \param _ObservedValues ref to set of observed values for this instance
+   * \param _board ref to InstanceBoard for callbacks on occasion of subjectKilled()
    * \param _parent Qt parent to automatically destroy when parent is destroyed
    */
   QtObservedAtom(
-      const ObservedValues_t &_obsvalues,
+      const ObservedValues_t &_ObservedValues,
+      QtObservedInstanceBoard &_board,
       QWidget * _parent=0);
 
@@ -71 +83 @@
   void recieveNotification(Observable *publisher, Notification_ptr notification);
 
+  /** Getter to atom index contained in \a ObservedValues.
+   *
+   * \return atom's index
+   */
+  atomId_t getAtomIndex() const;
+
+  /** Getter to atom position contained in \a ObservedValues.
+   *
+   * \return atom's position
+   */
+  Vector getAtomPosition() const;
+
+  /** Getter to atom element contained in \a ObservedValues.
+   *
+   * \return atom's elemnt
+   */
+  atomicNumber_t getAtomElement() const;
+
+  //!> typedef for list of bonds, defined by pairs of atom ids
+  typedef std::vector< std::pair<atomId_t, atomId_t> > ListOfBonds_t;
+
+  /** Getter to atom bonds contained in \a ObservedValues.
+   *
+   * \return atom's bonds
+   */
+  ListOfBonds_t getAtomBonds() const;
+
 signals:
-
-private slots:
-
-
-private:
+  void indexChanged();
+  void positionChanged();
+  void elementChanged();
+  void bondsChanged();
+
+//private slots:
+
+private:
+  void activateObserver();
+  void deactivateObserver();
+
+  static const atom * const getAtomConst(const atomId_t _id);
+  static atom * const getAtom(const atomId_t _id);
+
+private:
+  static atomId_t updateIndex();
+  static Vector updatePosition(
+      const boost::function<const atomId_t ()> &_getAtomIndex);
+  static atomicNumber_t updateElement(
+      const boost::function<const atomId_t ()> &_getAtomIndex);
+  static ListOfBonds_t updateBonds(
+      const boost::function<const atomId_t ()> &_getAtomIndex);
+
+  //!> enumeration of observed values to match with entries in ObservedValues
+  enum ObservedTypes {
+    //!> contains the current atom index
+    AtomIndex,
+    //!> contains the current atom position
+    AtomPosition,
+    //!> contains the current atom element
+    AtomElement,
+    //!> contains the current set of bonds atoms fort the atom
+    AtomBonds,
+    //!> gives the size of the enumeration
+    MAX_ObservedTypes
+  };
+
+  /** Initializes all \a ObservedValues entries.
+   *
+   * \param _ObservedValues vector of ObservedValue to be filled
+   * \param _id atom id
+   * \param _atomref reference to atom
+   * \param _subjectKilled ref to function to call on subjectKilled()
+   */
+  static void initObservedValues(
+      ObservedValues_t &_ObservedValues,
+      const atomId_t _id,
+      const atom * const _atomref,
+      const boost::function<void(const atomId_t)> &_subjectKilled);
+
+  /** Destroys all \a ObservedValues entries.
+   *
+   * \param _ObservedValues vector of ObservedValue to be destroyed
+   */
+  static void destroyObservedValues(
+      std::vector<boost::any> &_ObservedValues);
+
+  //!> counts how many ObservedValues have already been subjectKilled()
+  mutable size_t subjectKilledCount;
+
+private:
+
+  //!> list of channels when index needs to update
+  static const Observable::channels_t AtomIndexChannels;
+  //!> list of channels when position needs to update
+  static const Observable::channels_t AtomPositionChannels;
+  //!> list of channels when element needs to update
+  static const Observable::channels_t AtomElementChannels;
+  //!> list of channels when bonds needs to update
+  static const Observable::channels_t AtomBondsChannels;
+
+  //!> we get multiple subjectKilled(), count and call callback() only on last
+  const unsigned int AllsignedOnChannels;
+  unsigned int signedOffChannels;
+
+  //!> the Observable we are signed on, also indicates whether we are sign on (not NULL)
+  const Observable *owner;
+
+private:
+
+  //!> reference to InstanceBoard for callbacks on subjectKilled()
+  QtObservedInstanceBoard & board;
+
   //!> internal reference to ObservedValues held by QtObservedInstanceBoard
-  const ObservedValues_t &obsvalues;
+  ObservedValues_t ObservedValues;
 };
 

src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp

@@ -36 +36 @@
 #include "QtObservedInstanceBoard.hpp"
 
-#include "UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp"
 #include "UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp"
+#include "UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp"
 
 #include "CodePatterns/MemDebug.hpp"
@@ -54 +54 @@
   Observer("QtObservedInstanceBoard"),
   WorldSignedOn(false),
-  atomObservedValues("atom"),
-  moleculeObservedValues("molecule"),
+  atomObservedValues("atom", *this),
+  moleculeObservedValues("molecule", *this),
   atomSubjectKilled(
       boost::bind(&QtObservedInstanceBoard::atomcountsubjectKilled, this, _1)),
@@ -181 +181 @@
             getAtom(AtomById(_id));
         if (_atom!= NULL) {
-          ObservedValues_t ObservedValues(GLMoleculeObject_atom::MAX_ObservedTypes);
+          ObservedValues_t ObservedValues(QtObservedAtom::MAX_ObservedTypes);
           LOG(3, "DEBUG: InformationBoard initializes ObservedValues for atom " << _id);
-          GLMoleculeObject_atom::initObservedValues(
+          QtObservedAtom::initObservedValues(
               ObservedValues,
               _id,
@@ -303 +303 @@
   ++(iter->second);
 
-  if (iter->second > GLMoleculeObject_atom::MAX_ObservedTypes) {
+  if (iter->second > QtObservedAtom::MAX_ObservedTypes) {
     ASSERT( atomObservedValues.getRefCount(_atomid) == 0,
         "QtObservedInstanceBoard::atomcountsubjectKilled() - observed Values for atom "

src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp

@@ -30 +30 @@
 
 class GLWorldScene;
-class GLMoleculeObject_atom;
 class GLMoleculeObject_bond;
 class GLMoleculeObject_molecule;
@@ -101 +100 @@
 private:
   friend class GLWorldScene;
-  friend class GLMoleculeObject_atom;
   friend class GLMoleculeObject_bond;
   friend class GLMoleculeObject_molecule;
+  friend class QtObservedAtom;
 
   //!> indicating whether we are still signedOn to World or not

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp

@@ -45 +45 @@
 
 #include <algorithm>
-#include <boost/assign.hpp>
 
 #include "Atom/atom.hpp"
 #include "Bond/bond.hpp"
-#include "Descriptors/AtomIdDescriptor.hpp"
 #include "Element/element.hpp"
 #include "Element/periodentafel.hpp"
@@ -56 +54 @@
 #include "UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp"
 #include "World.hpp"
-#include "WorldTime.hpp"
-
-#include "ObservedValue_wCallback.hpp"
-
-using namespace boost::assign;
-
-static const Observable::channels_t getAtomBondsChannels()
-{
-  Observable::channels_t channels;
-  channels += AtomObservable::BondsAdded, AtomObservable::BondsRemoved;
-  return channels;
-}
-
-static const Observable::channels_t getAllObservedChannels()
-{
-  Observable::channels_t channels;
-  channels +=
-      AtomObservable::IndexChanged,
-      AtomObservable::PositionChanged,
-      AtomObservable::ElementChanged,
-      AtomObservable::BondsAdded,
-      AtomObservable::BondsRemoved;
-  return channels;
-}
-
-// static entities
-const Observable::channels_t
-GLMoleculeObject_atom::AtomIndexChannels(1, AtomObservable::IndexChanged);
-const Observable::channels_t
-GLMoleculeObject_atom::AtomPositionChannels(1, AtomObservable::PositionChanged);
-const Observable::channels_t
-GLMoleculeObject_atom::AtomElementChannels(1, AtomObservable::ElementChanged);
-const Observable::channels_t
-GLMoleculeObject_atom::AtomBondsChannels(getAtomBondsChannels());
 
 GLMoleculeObject_atom::GLMoleculeObject_atom(
     QGLSceneNode *mesh[],
     QObject *parent,
-    const atomId_t _id,
-    QtObservedInstanceBoard * _board,
-    std::vector<boost::any> _ObservedValues) :
+    QtObservedAtom::ptr _ObservedAtom) :
   GLMoleculeObject(mesh, parent),
-  Observer(std::string("GLMoleculeObject_atom")+toString(_id)),
-  atomref(getAtom(_id)),
-  ObservedValues(_ObservedValues),
-  subjectKilledCount(0),
-  owner(NULL),
-  AllsignedOnChannels(getAllObservedChannels().size()),
-  signedOnChannels(0),
-  board(_board)
+  ObservedAtom(_ObservedAtom)
 {
-  init(_id);
+  init(ObservedAtom->getAtomIndex());
 }
 
@@ -118 +73 @@
   m_selected = const_cast<const World &>(World::getInstance()).isAtomSelected(_id);
 
-  // sign On
-  activateObserver();
-
-  // atomref is only used for caching the ref, it must be used elswhere
-  const_cast<atom *&>(atomref) = NULL;
-
   connect( this, SIGNAL(clicked()), this, SLOT(wasClicked()));
-  connect( this, SIGNAL(idChanged()), this, SLOT(resetIndex()), Qt::QueuedConnection);
-  connect( this, SIGNAL(elementChanged()), this, SLOT(resetElement()), Qt::QueuedConnection);
-  connect( this, SIGNAL(positionChanged()), this, SLOT(resetPosition()), Qt::QueuedConnection);
-  connect( this, SIGNAL(bondsChanged()), this, SLOT(resetPosition()), Qt::QueuedConnection);
+  connect( ObservedAtom.get(), SIGNAL(indexChanged()), this, SLOT(resetIndex()));
+  connect( ObservedAtom.get(), SIGNAL(elementChanged()), this, SLOT(resetElement()));
+  connect( ObservedAtom.get(), SIGNAL(positionChanged()), this, SLOT(resetPosition()));
+  connect( ObservedAtom.get(), SIGNAL(bondsChanged()), this, SLOT(resetPosition()));
 
   // use that ObservedValues::AtomBonds is always up-to-date
@@ -134 +83 @@
 }
 
-void GLMoleculeObject_atom::activateObserver()
-{
-  if (atomref != NULL) {
-    Observable::channels_t channels = getAllObservedChannels();
-    owner = static_cast<const Observable *>(atomref);
-    for (Observable::channels_t::const_iterator iter = channels.begin();
-        iter != channels.end(); ++iter)
-      owner->signOn(this, *iter);
-  }
-}
-
-
-void GLMoleculeObject_atom::deactivateObserver()
-{
-  // sign Off
-  if (owner != NULL) {
-    Observable::channels_t channels = getAllObservedChannels();
-    for (Observable::channels_t::const_iterator iter = channels.begin();
-        iter != channels.end(); ++iter)
-      owner->signOff(this, *iter);
-    owner = NULL;
-    signedOnChannels = 0;
-  }
-}
-
 GLMoleculeObject_atom::~GLMoleculeObject_atom()
-{
-  deactivateObserver();
-  board->returnAtomObservedValues(getAtomIndex(), ObservedValues);
-}
+{}
 
 void GLMoleculeObject_atom::resetIndex()
 {
-  const atomId_t newId = getAtomIndex();
+  const atomId_t newId = ObservedAtom->getAtomIndex();
   const size_t oldId = objectId();
   ASSERT( newId != oldId,
@@ -173 +94 @@
   LOG(4, "INFO: GLMoleculeObject_atom::resetIndex() - new index is "+toString(newId)+".");
   setObjectId(newId);
-
-  emit indexChanged(this, oldId, newId);
 }
 
 void GLMoleculeObject_atom::resetPosition()
 {
-  const Vector Position = getAtomPosition();
+  const Vector Position = ObservedAtom->getAtomPosition();
   LOG(4, "INFO: GLMoleculeObject_atom::resetIndex() - new position is "+toString(Position)+".");
   setPosition(QVector3D(Position[0], Position[1], Position[2]));
@@ -188 +107 @@
   size_t elementno = 0;
   const element * const _type = World::getInstance().
-      getPeriode()->FindElement(getAtomElement());
+      getPeriode()->FindElement(ObservedAtom->getAtomElement());
   if (_type != NULL) {
     elementno = _type->getAtomicNumber();
@@ -214 +133 @@
 void GLMoleculeObject_atom::resetBonds()
 {
-  ListOfBonds_t ListOfBonds_new = getAtomBonds();
+  QtObservedAtom::ListOfBonds_t ListOfBonds_new = ObservedAtom->getAtomBonds();
   std::sort(ListOfBonds_new.begin(), ListOfBonds_new.end());
-  ListOfBonds_t BondsToAdd;
+  QtObservedAtom::ListOfBonds_t BondsToAdd;
   std::set_difference(
       ListOfBonds_new.begin(), ListOfBonds_new.end(),
       ListOfBonds.begin(), ListOfBonds.end(),
       std::back_inserter(BondsToAdd));
-  ListOfBonds_t BondsToRemove;
+  QtObservedAtom::ListOfBonds_t BondsToRemove;
   std::set_difference(
       ListOfBonds.begin(), ListOfBonds.end(),
       ListOfBonds_new.begin(), ListOfBonds_new.end(),
       std::back_inserter(BondsToRemove));
-  for (ListOfBonds_t::const_iterator iter = BondsToAdd.begin();
+  for (QtObservedAtom::ListOfBonds_t::const_iterator iter = BondsToAdd.begin();
       iter != BondsToAdd.end();
       ++iter) {
-    const GLMoleculeObject_bond::SideOfBond side = (iter->first == getAtomIndex()) ?
+    const GLMoleculeObject_bond::SideOfBond side = (iter->first == ObservedAtom->getAtomIndex()) ?
         GLMoleculeObject_bond::left : GLMoleculeObject_bond::right;
     emit BondsAdded(iter->first, iter->second, side);
   }
-  for (ListOfBonds_t::const_iterator iter = BondsToRemove.begin();
+  for (QtObservedAtom::ListOfBonds_t::const_iterator iter = BondsToRemove.begin();
       iter != BondsToRemove.end();
       ++iter) {
@@ -268 +187 @@
 void GLMoleculeObject_atom::wasClicked()
 {
-  LOG(4, "INFO: GLMoleculeObject_atom: atom " << getAtomIndex() << " has been clicked");
-  emit clicked(getAtomIndex());
+  LOG(4, "INFO: GLMoleculeObject_atom: atom "
+      << ObservedAtom->getAtomIndex() << " has been clicked");
+  emit clicked(ObservedAtom->getAtomIndex());
 }
-
-const atom * const GLMoleculeObject_atom::getAtomConst(const atomId_t _id)
-{
-  const atom * const _atom = const_cast<const World &>(World::getInstance()).
-      getAtom(AtomById(_id));
-  return _atom;
-}
-
-atom * const GLMoleculeObject_atom::getAtom(const atomId_t _id)
-{
-  atom * const _atom = World::getInstance().getAtom(AtomById(_id));
-  return _atom;
-}
-
-atomId_t GLMoleculeObject_atom::updateIndex()
-{
-  return const_cast<const World &>(World::getInstance()).lastChangedAtomId();
-}
-
-Vector GLMoleculeObject_atom::updatePosition(
-    const boost::function<const atomId_t ()> &_getAtomIndex)
-{
-  const atom * const _atom = getAtomConst(_getAtomIndex());
-  if (_atom != NULL) {
-    return _atom->getPosition();
-  } else {
-    return zeroVec;
-  }
-}
-
-atomicNumber_t GLMoleculeObject_atom::updateElement(
-    const boost::function<const atomId_t ()> &_getAtomIndex)
-{
-  const atom * const _atom = getAtomConst(_getAtomIndex());
-  if (_atom != NULL) {
-    return _atom->getElementNo();
-  } else {
-    return (atomicNumber_t)-1;
-  }
-}
-
-GLMoleculeObject_atom::ListOfBonds_t GLMoleculeObject_atom::updateBonds(
-    const boost::function<const atomId_t ()> &_getAtomIndex)
-{
-  ListOfBonds_t ListOfBonds;
-  const atom * const _atom = getAtomConst(_getAtomIndex());
-  if (_atom != NULL) {
-    // make sure bonds is up-to-date
-    const BondList ListBonds = _atom->getListOfBonds();
-    for (BondList::const_iterator iter = ListBonds.begin();
-        iter != ListBonds.end();
-        ++iter)
-      ListOfBonds.insert( ListOfBonds.end(), std::make_pair(
-          (*iter)->leftatom->getId(),
-          (*iter)->rightatom->getId()) );
-  } else {
-    ELOG(2, "Atom with id "+toString(_getAtomIndex())+" is already gone.");
-  }
-  return ListOfBonds;
-}
-
-void GLMoleculeObject_atom::update(Observable *publisher)
-{
-  ASSERT(0, "GLMoleculeObject_atom::update() - we are not signed on for global updates.");
-}
-
-void GLMoleculeObject_atom::subjectKilled(Observable *publisher)
-{
-  ++signedOnChannels;
-
-  if (signedOnChannels == AllsignedOnChannels) {
-    // remove owner: no more signOff needed
-    owner = NULL;
-
-    board->atomcountsubjectKilled(getAtomIndex());
-  }
-}
-
-void GLMoleculeObject_atom::recieveNotification(Observable *publisher, Notification_ptr notification)
-{
-  // ObservedValues have been updated before, hence convert updates to Qt's signals
-  atom * const _atom = dynamic_cast<atom *>(publisher);
-  if (_atom != NULL) {
-    switch (notification->getChannelNo()) {
-      case AtomObservable::IndexChanged:
-        emit idChanged();
-        break;
-      case AtomObservable::PositionChanged:
-        emit positionChanged();
-        break;
-      case AtomObservable::ElementChanged:
-        emit elementChanged();
-        break;
-      case AtomObservable::BondsAdded:
-      case AtomObservable::BondsRemoved:
-        emit bondsChanged();
-        break;
-      default:
-        ASSERT(0, "GLMoleculeObject_atom::recieveNotification() - we are not signed on to channel "
-            +toString(notification->getChannelNo())+" of the atom.");
-        break;
-    }
-  } else
-    ASSERT(0, "GLMoleculeObject_atom::recieveNotification() - received notification from unexpected source.");
-}
-
-void GLMoleculeObject_atom::initObservedValues(
-    std::vector<boost::any> &_ObservedValues,
-    const atomId_t _id,
-    const atom * const _atomref,
-    const boost::function<void(const atomId_t)> &_subjectKilled)
-{
-  /* This is an old note from when the code was still part of cstor's initializer body.
-   * TODO: Probably does not apply anymore but has not yet been tested.
-   *
-   * We must not use boost::cref(this) as "this" has not been properly constructed and seemingly
-   * boost::cref tries to do some magic to grasp the inheritance hierarchy which fails because
-   * the class has not been fully constructed yet. "This" itself seems to be working fine.
-   */
-
-  ASSERT( _ObservedValues.size() == MAX_ObservedTypes,
-      "GLMoleculeObject_atom::initObservedValues() - given ObservedValues has not correct size.");
-
-  // fill ObservedValues: index first
-  const boost::function<atomId_t ()> AtomIndexUpdater(
-      boost::bind(&GLMoleculeObject_atom::updateIndex));
-
-  ObservedValue_wCallback<atomId_t> * const IndexObservable =
-      new ObservedValue_wCallback<atomId_t>(
-          _atomref,
-          boost::bind(&GLMoleculeObject_atom::updateIndex),
-          "AtomIndex_"+toString(_id),
-          _id,
-          AtomIndexChannels,
-          _subjectKilled);
-  _ObservedValues[AtomIndex] = IndexObservable;
-
-  const boost::function<const atomId_t ()> AtomIndexGetter =
-      boost::bind(&ObservedValue_wCallback<atomId_t>::get,
-          IndexObservable);
-
-  // fill ObservedValues: then all the other that need index
-  const boost::function<Vector ()> AtomPositionUpdater(
-      boost::bind(&GLMoleculeObject_atom::updatePosition, AtomIndexGetter));
-  const boost::function<atomicNumber_t ()> AtomElementUpdater(
-      boost::bind(&GLMoleculeObject_atom::updateElement, AtomIndexGetter));
-  const boost::function<ListOfBonds_t ()> AtomBondsUpdater(
-      boost::bind(&GLMoleculeObject_atom::updateBonds, AtomIndexGetter));
-
-  _ObservedValues[AtomPosition] = new ObservedValue_wCallback<Vector, atomId_t>(
-      _atomref,
-      AtomPositionUpdater,
-      "AtomPosition_"+toString(_id),
-      AtomPositionUpdater(),
-      AtomPositionChannels,
-      _subjectKilled,
-      AtomIndexGetter);
-  _ObservedValues[AtomElement] = new ObservedValue_wCallback<atomicNumber_t, atomId_t>(
-      _atomref,
-      AtomElementUpdater,
-      "AtomElement"+toString(_id),
-      AtomElementUpdater(),
-      AtomElementChannels,
-      _subjectKilled,
-      AtomIndexGetter);
-  _ObservedValues[AtomBonds] = new ObservedValue_wCallback<ListOfBonds_t, atomId_t>(
-      _atomref,
-      AtomBondsUpdater,
-      "AtomBonds_"+toString(_id),
-      AtomBondsUpdater(),
-      AtomBondsChannels,
-      _subjectKilled,
-      AtomIndexGetter);
-}
-
-void GLMoleculeObject_atom::destroyObservedValues(
-    std::vector<boost::any> &_ObservedValues)
-{
-  delete boost::any_cast<ObservedValue_wCallback<atomId_t> *>(_ObservedValues[AtomIndex]);
-  delete boost::any_cast<ObservedValue_wCallback<Vector, atomId_t> *>(_ObservedValues[AtomPosition]);
-  delete boost::any_cast<ObservedValue_wCallback<atomicNumber_t, atomId_t> *>(_ObservedValues[AtomElement]);
-  delete boost::any_cast<ObservedValue_wCallback<ListOfBonds_t, atomId_t> *>(_ObservedValues[AtomBonds]);
-  _ObservedValues.clear();
-}
-
-atomId_t GLMoleculeObject_atom::getAtomIndex() const
-{
-  return boost::any_cast<ObservedValue_wCallback<atomId_t> *>(ObservedValues[AtomIndex])->get();
-}
-
-Vector GLMoleculeObject_atom::getAtomPosition() const
-{
-  return boost::any_cast<ObservedValue_wCallback<Vector, atomId_t> *>(ObservedValues[AtomPosition])->get();
-}
-
-atomicNumber_t GLMoleculeObject_atom::getAtomElement() const
-{
-  return boost::any_cast<ObservedValue_wCallback<atomicNumber_t, atomId_t> *>(ObservedValues[AtomElement])->get();
-}
-
-GLMoleculeObject_atom::ListOfBonds_t GLMoleculeObject_atom::getAtomBonds() const
-{
-  return boost::any_cast<ObservedValue_wCallback<ListOfBonds_t, atomId_t> *>(ObservedValues[AtomBonds])->get();
-}

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp

@@ -20 +20 @@
 
 #include "CodePatterns/ObservedValue.hpp"
-#include "CodePatterns/Observer/Observer.hpp"
 
-#include "LinearAlgebra/Vector.hpp"
-
-#include "Bond/bond.hpp"
 #include "UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp"
+#include "UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp"
 #include "types.hpp"
 
@@ -31 +28 @@
 class QtObservedInstanceBoard;
 
-class GLMoleculeObject_atom : public GLMoleculeObject, Observer
+class GLMoleculeObject_atom : public GLMoleculeObject
 {
   Q_OBJECT
@@ -38 +35 @@
       QGLSceneNode *mesh[],
       QObject *parent,
-      const atomId_t id,
-      QtObservedInstanceBoard * _board,
-      std::vector<boost::any> _ObservedValues
+      QtObservedAtom::ptr _ObservedAtom
       );
   virtual ~GLMoleculeObject_atom();
 
   void draw(QGLPainter *painter, const QVector4D &cameraPlane);
-
-  // Observer functions
-  void update(Observable *publisher);
-  void subjectKilled(Observable *publisher);
-  void recieveNotification(Observable *publisher, Notification_ptr notification);
 
 public slots:
@@ -67 +57 @@
   void BondsRemoved(const atomId_t _left, const atomId_t _right);
   void indexChanged(GLMoleculeObject_atom *ob, const atomId_t oldId, const atomId_t newId);
-  void idChanged();
-  void positionChanged();
-  void elementChanged();
-  void bondsChanged();
 
 private:
-  //!> grant GLMoleculeObject_molecule acess to reset functions
-  friend class GLMoleculeObject_molecule;
-
-  //!> typedef for list of bonds, defined by pairs of atom ids
-  typedef std::vector< std::pair<atomId_t, atomId_t> > ListOfBonds_t;
-
-  static const atom * const getAtomConst(const atomId_t _id);
-  static atom * const getAtom(const atomId_t _id);
-
-  static atomId_t updateIndex();
-  static Vector updatePosition(
-      const boost::function<const atomId_t ()> &_getAtomIndex);
-  static atomicNumber_t updateElement(
-      const boost::function<const atomId_t ()> &_getAtomIndex);
-  static ListOfBonds_t updateBonds(
-      const boost::function<const atomId_t ()> &_getAtomIndex);
-
-  void activateObserver();
-  void deactivateObserver();
-
   void init(const atomId_t _id);
 
 private:
+  //!> current list of bonds to compare new onw against for changes
+  QtObservedAtom::ListOfBonds_t ListOfBonds;
 
-  //!> current list of bonds to compare new onw against for changes
-  ListOfBonds_t ListOfBonds;
-
-  //!> temporary variable used in cstor
-  atom * const atomref;
-
-private:
-  friend class QtObservedInstanceBoard;
-  /** Observed Values **/
-
-  //!> enumeration of observed values to match with entries in ObservedValues
-  enum ObservedTypes {
-    //!> contains the current atom index
-    AtomIndex,
-    //!> contains the current atom position
-    AtomPosition,
-    //!> contains the current atom element
-    AtomElement,
-    //!> contains the current set of bonds atoms fort the atom
-    AtomBonds,
-    //!> gives the size of the enumeration
-    MAX_ObservedTypes
-  };
-
-  //!> vector with all observed values
-  std::vector<boost::any> ObservedValues;
-
-  /** Initializes all \a ObservedValues entries.
-   *
-   * \param _ObservedValues vector of ObservedValue to be filled
-   * \param _id atom id
-   * \param _atomref reference to atom
-   * \param _subjectKilled ref to function to call on subjectKilled()
-   */
-  static void initObservedValues(
-      std::vector<boost::any> &_ObservedValues,
-      const atomId_t _id,
-      const atom * const _atomref,
-      const boost::function<void(const atomId_t)> &_subjectKilled);
-
-  /** Destroys all \a ObservedValues entries.
-   *
-   * \param _ObservedValues vector of ObservedValue to be destroyed
-   */
-  static void destroyObservedValues(
-      std::vector<boost::any> &_ObservedValues);
-
-  /** Getter to atom index contained in \a ObservedValues.
-   *
-   * \return atom's index
-   */
-  atomId_t getAtomIndex() const;
-
-  /** Getter to atom position contained in \a ObservedValues.
-   *
-   * \return atom's position
-   */
-  Vector getAtomPosition() const;
-
-  /** Getter to atom element contained in \a ObservedValues.
-   *
-   * \return atom's elemnt
-   */
-  atomicNumber_t getAtomElement() const;
-
-  /** Getter to atom bonds contained in \a ObservedValues.
-   *
-   * \return atom's bonds
-   */
-  ListOfBonds_t getAtomBonds() const;
-
-  //!> counts how many ObservedValues have already been subjectKilled()
-  mutable size_t subjectKilledCount;
-
-private:
-
-  //!> list of channels when index needs to update
-  static const Observable::channels_t AtomIndexChannels;
-  //!> list of channels when position needs to update
-  static const Observable::channels_t AtomPositionChannels;
-  //!> list of channels when element needs to update
-  static const Observable::channels_t AtomElementChannels;
-  //!> list of channels when bonds needs to update
-  static const Observable::channels_t AtomBondsChannels;
-
-  //!> the Observable we are signed on, also indicates whether we are sign on (not NULL)
-  const Observable *owner;
-
-  //!> we get multiple subjectKilled(), count and call callback() only on last
-  const unsigned int AllsignedOnChannels;
-  unsigned int signedOnChannels;
-
-  QtObservedInstanceBoard * board;
+  QtObservedAtom::ptr ObservedAtom;
 };
 

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp

@@ -573 +573 @@
           GLMoleculeObject::meshSphere,
           this,
-          _id,
-          board,
-          board->getAtomObservedValues(_id));
+          board->getObservedAtom(_id));
   ASSERT( atomObject != NULL,
       "GLMoleculeObject_molecule::atomInserted - could not create atom object for "+toString(_id));