source: src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp@ 15c8a9

/*
 * 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/>.
 */

/*
 * GLMoleculeObject_atom.cpp
 *
 *  Created on: Aug 17, 2011
 *      Author: heber
 */

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

#include "GLMoleculeObject_atom.hpp"

#include <Qt3D/qglscenenode.h>

#include "CodePatterns/MemDebug.hpp"

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

#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"
#include "LinearAlgebra/Vector.hpp"
#include "GLMoleculeObject_bond.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 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) :
  GLMoleculeObject(mesh, parent),
  Observer(std::string("GLMoleculeObject_atom")+toString(_id)),
  atomref(getAtom(_id)),
  ObservedValues(MAX_ObservedTypes),
  subjectKilledCount(0),
  owner(NULL)
{
  boost::function<void(const atomId_t)> subjectKilled =
      boost::bind(&GLMoleculeObject_atom::countsubjectKilled, this, _id);
  initObservedValues(ObservedValues, _id, atomref, subjectKilled);

  init(_id);
}

GLMoleculeObject_atom::GLMoleculeObject_atom(
    QGLSceneNode *mesh[],
    QObject *parent,
    const atomId_t _id,
    std::vector<boost::any> _ObservedValues) :
  GLMoleculeObject(mesh, parent),
  Observer(std::string("GLMoleculeObject_atom")+toString(_id)),
  atomref(getAtom(_id)),
  ObservedValues(_ObservedValues),
  subjectKilledCount(0),
  owner(NULL)
{
  init(_id);
}

void GLMoleculeObject_atom::init(const atomId_t _id)
{
  setObjectId(_id);
  resetPosition();
  resetElement();

  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);
}

void GLMoleculeObject_atom::activateObserver()
{
  if (atomref != NULL) {
    owner = static_cast<const Observable *>(atomref);
    owner->signOn(this, AtomObservable::IndexChanged);
    owner->signOn(this, AtomObservable::PositionChanged);
    owner->signOn(this, AtomObservable::ElementChanged);
    owner->signOn(this, AtomObservable::BondsAdded);
    owner->signOn(this, AtomObservable::BondsRemoved);
  }
}


void GLMoleculeObject_atom::deactivateObserver()
{
  // sign Off
  if (owner != NULL) {
    owner->signOff(this, AtomObservable::IndexChanged);
    owner->signOff(this, AtomObservable::PositionChanged);
    owner->signOff(this, AtomObservable::ElementChanged);
    owner->signOff(this, AtomObservable::BondsAdded);
    owner->signOff(this, AtomObservable::BondsRemoved);
    owner = NULL;
  }
}

GLMoleculeObject_atom::~GLMoleculeObject_atom()
{
  deactivateObserver();
  destroyObservedValues(ObservedValues);
}

void GLMoleculeObject_atom::resetIndex()
{
  const atomId_t newId = getAtomIndex();
  const size_t oldId = objectId();
  ASSERT( newId != oldId,
      "GLMoleculeObject_atom::updateIndex() - index "+toString(newId)+" did not change.");
  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();
  LOG(4, "INFO: GLMoleculeObject_atom::resetIndex() - new position is "+toString(Position)+".");
  setPosition(QVector3D(Position[0], Position[1], Position[2]));
}

void GLMoleculeObject_atom::resetElement()
{
  size_t elementno = 0;
  const element * const _type = World::getInstance().
      getPeriode()->FindElement(getAtomElement());
  if (_type != NULL) {
    elementno = _type->getAtomicNumber();
  } else { // if no element yet, set to hydrogen
    elementno = 1;
  }
  LOG(4, "INFO: GLMoleculeObject_atom::resetIndex() - new element number is "+toString(elementno)+".");

  // set materials
  QGLMaterial *elementmaterial = getMaterial(elementno);
  ASSERT(elementmaterial != NULL,
      "GLMoleculeObject_atom::GLMoleculeObject_atom() - QGLMaterial ref from getter function is NULL.");
  setMaterial(elementmaterial);

  // set scale
  double radius = 0.;
  if (_type != NULL) {
    radius = _type->getVanDerWaalsRadius();
  } else {
    radius = 0.5;
  }
  setScale( radius / 4. );
}

void GLMoleculeObject_atom::resetBonds()
{
  ListOfBonds_t ListOfBonds_new = getAtomBonds();
  std::sort(ListOfBonds_new.begin(), ListOfBonds_new.end());
  ListOfBonds_t BondsToAdd;
  std::set_difference(
      ListOfBonds_new.begin(), ListOfBonds_new.end(),
      ListOfBonds.begin(), ListOfBonds.end(),
      std::back_inserter(BondsToAdd));
  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();
      iter != BondsToAdd.end();
      ++iter) {
    const GLMoleculeObject_bond::SideOfBond side = (iter->first == getAtomIndex()) ?
        GLMoleculeObject_bond::left : GLMoleculeObject_bond::right;
    emit BondsAdded(iter->first, iter->second, side);
  }
  for (ListOfBonds_t::const_iterator iter = BondsToRemove.begin();
      iter != BondsToRemove.end();
      ++iter) {
    emit BondsRemoved(iter->first, iter->second);
  }
  ListOfBonds = ListOfBonds_new;
}

void GLMoleculeObject_atom::Selected()
{
  ASSERT( !m_selected,
      "GLMoleculeObject_atom::Selected() - 3D rep of atom is already selected.");
  m_selected = true;

  emit changed();
}

void GLMoleculeObject_atom::Unselected()
{
  ASSERT( m_selected,
      "GLMoleculeObject_atom::Unselected() - 3D rep of atom is already unselected.");
  m_selected = false;

  emit changed();
}


void GLMoleculeObject_atom::draw(QGLPainter *painter, const QVector4D &cameraPlane)
{
  // call old hook to do the actual paining
  GLMoleculeObject::draw(painter, cameraPlane);
}

void GLMoleculeObject_atom::wasClicked()
{
  LOG(4, "INFO: GLMoleculeObject_atom: atom " << getAtomIndex() << " has been clicked");
  emit clicked(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)
{
  deactivateObserver();

  countsubjectKilled(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::countsubjectKilled(const atomId_t)
{
  ++subjectKilledCount;

  if (subjectKilledCount > ObservedValues.size())
    emit InstanceRemoved(getAtomIndex());
}

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();
}