source: src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp@ 739ee9

/*
 * 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_molecule.cpp
 *
 *  Created on: Mar 30, 2012
 *      Author: ankele
 */





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

#include "GLMoleculeObject_molecule.hpp"

#include <Qt3D/qglscenenode.h>

#include "CodePatterns/MemDebug.hpp"

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

#include "Atom/atom.hpp"
#include "molecule.hpp"
#include "Descriptors/AtomIdDescriptor.hpp"
#include "Element/element.hpp"
#include "LinearAlgebra/Vector.hpp"
#include "World.hpp"

#include "GLMoleculeObject_atom.hpp"

GLMoleculeObject_molecule::GLMoleculeObject_molecule(QGLSceneNode *mesh[], QObject *parent, const molecule *molref) :
  GLMoleculeObject(mesh, parent),
  Observer(std::string("GLMoleculeObject_molecule")+toString(molref->getId())),
  _molecule(molref),
  hoverAtom(NULL)
{
  // sign on as observer (obtain non-const instance before)
  _molecule->signOn(this, molecule::AtomInserted);
  _molecule->signOn(this, molecule::AtomRemoved);
  /*molref->signOn(this, AtomObservable::IndexChanged);
  molref->signOn(this, AtomObservable::PositionChanged);
  molref->signOn(this, AtomObservable::ElementChanged);
  molref->signOn(this, AtomObservable::BondsAdded);*/
  setMaterial(getMaterial(1));
  World::getInstance().signOn(this, World::SelectionChanged);
  updateBoundingBox();

  // initially, atoms and bonds should be visible
  m_visible = false;

  init();
}

GLMoleculeObject_molecule::~GLMoleculeObject_molecule()
{
  _molecule->signOff(this, molecule::AtomInserted);
  _molecule->signOff(this, molecule::AtomRemoved);
  /*_atom->signOff(this, AtomObservable::IndexChanged);
  _atom->signOff(this, AtomObservable::PositionChanged);
  _atom->signOff(this, AtomObservable::ElementChanged);
  _atom->signOff(this, AtomObservable::BondsAdded);*/
  World::getInstance().signOff(this, World::SelectionChanged);
}

/** Initialise the WorldScene with molecules and atoms from World.
 *
 */
void GLMoleculeObject_molecule::init()
{
  if (_molecule->begin() != _molecule->end()) {
    for (molecule::const_iterator atomiter = _molecule->begin();
        atomiter != _molecule->end();
        atomiter++) {
      // create atom objects in scene
      atomInserted((*atomiter)->getId());

      // create bond objects in scene
      const BondList &bondlist = (*atomiter)->getListOfBonds();
      for (BondList::const_iterator bonditer = bondlist.begin();
          bonditer != bondlist.end();
          ++bonditer) {
        const bond::ptr _bond = *bonditer;
        const GLMoleculeObject_bond::SideOfBond side = (_bond->leftatom == *atomiter) ?
            GLMoleculeObject_bond::left : GLMoleculeObject_bond::right;
        bondInserted(_bond, side);
      }
    }
  }
}

void GLMoleculeObject_molecule::addAtomBonds(
    const bond::ptr &_bond,
    const GLMoleculeObject_bond::SideOfBond _side
    )
{
  bool bond_present = false;
  const BondIds ids = getBondIds(_bond, _side);
  // check whether bond is not present already
  bond_present = BondsinSceneMap.count(ids);
  if (!bond_present)
    bondInserted(_bond, _side);
  else {
    BondsinSceneMap[ids]->resetPosition();
    BondsinSceneMap[ids]->resetWidth();
  }
}

void GLMoleculeObject_molecule::addAtomBonds(
    const atom *_atom)
{
  const bool atom_present = AtomsinSceneMap.count(_atom->getId());
  const BondList &bondlist = _atom->getListOfBonds();
  for (BondList::const_iterator bonditer = bondlist.begin();
      (bonditer != bondlist.end()) && atom_present;
      ++bonditer) {
    const bond::ptr _bond = *bonditer;
    // check if OtherAtom's sphere is already present
    const atom *OtherAtom = _bond->GetOtherAtom(_atom);
    const bool otheratom_present = AtomsinSceneMap.count(OtherAtom->getId());
    if (otheratom_present && atom_present) {
      const GLMoleculeObject_bond::SideOfBond side = (_bond->leftatom == _atom) ?
          GLMoleculeObject_bond::left : GLMoleculeObject_bond::right;
      const GLMoleculeObject_bond::SideOfBond otherside = (_bond->leftatom == _atom) ?
          GLMoleculeObject_bond::right : GLMoleculeObject_bond::left;
      addAtomBonds(_bond, side);
      addAtomBonds(_bond, otherside);
    }
  }
}

void GLMoleculeObject_molecule::reinit()
{
  if (_molecule->getAtomCount() > 0) {
    for (molecule::const_iterator atomiter = _molecule->begin();
        atomiter != _molecule->end();
        atomiter++) {
      // check whether atom already exists
      const atomId_t atomid = (*atomiter)->getId();
      const bool atom_present = AtomsinSceneMap.count(atomid);
      if (!atom_present)
        atomInserted((*atomiter)->getId());
      else
        AtomsinSceneMap[atomid]->resetPosition();


      // create bond objects in scene
      addAtomBonds(*atomiter);
    }
  }
}

void GLMoleculeObject_molecule::updateBoundingBox()
{
  Shape shape = _molecule->getBoundingSphere();
  Vector v = shape.getCenter();
  setPosition(QVector3D(v[0], v[1], v[2]));
  setScale(shape.getRadius() + 0.3); // getBoundingShape() only sees atoms as points, so make the box a bit bigger
}

void GLMoleculeObject_molecule::update(Observable *publisher)
{
#ifdef LOG_OBSERVER
  const molecule *_mol = static_cast<molecule *>(publisher);
  observerLog().addMessage() << "++ Update of Observer " << observerLog().getName(static_cast<Observer *>(this)) << " from molecule "+toString(_mol->getId())+".";
#endif
}

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

void GLMoleculeObject_molecule::recieveNotification(Observable *publisher, Notification_ptr notification)
{
  if (publisher == dynamic_cast<const Observable*>(_molecule)){
    // notofication from atom
#ifdef LOG_OBSERVER
    observerLog().addMessage() << "++ Update of Observer "<< observerLog().getName(static_cast<Observer *>(this))
          << " received notification from molecule " << _molecule->getId() << " for channel "
          << notification->getChannelNo() << ".";
#endif
    switch (notification->getChannelNo()) {
      case molecule::AtomInserted:
      {
        const atomId_t _id = _molecule->lastChanged()->getId();
  #ifdef LOG_OBSERVER
        observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that atom "+toString(_id)+" has been inserted.";
  #endif
        atomInserted(_id);
        break;
      }
      case World::AtomRemoved:
      {
        const atomId_t _id = _molecule->lastChanged()->getId();
  #ifdef LOG_OBSERVER
        observerLog().addMessage() << "++ Observer " << observerLog().getName(static_cast<Observer *>(this)) << " received notification that atom "+toString(_id)+" has been removed.";
  #endif
        atomRemoved(_id);
        break;
      }
      default:
        break;
    }
  }else{
    // notification from world
#ifdef LOG_OBSERVER
    observerLog().addMessage() << "++ Update of Observer "<< observerLog().getName(static_cast<Observer *>(this))
          << " received notification from world for channel "
          << notification->getChannelNo() << ".";
#endif
    switch (notification->getChannelNo()) {
      case World::SelectionChanged:
        setSelected(World::getInstance().isSelected(_molecule));
        break;
      default:
        break;
    }
  }
}

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

void GLMoleculeObject_molecule::draw(QGLPainter *painter, const QVector4D &cameraPlane)
{
  // draw either molecule's mesh or all atoms and bonds
  if (m_visible) {
    GLMoleculeObject::draw(painter, cameraPlane);
  } else {
    // 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);
    }
  }
}

/** Adds an atom of this molecule to the scene.
 *
 * @param _atom atom to add
 */
void GLMoleculeObject_molecule::atomInserted(const atomicNumber_t _id)
{
  LOG(3, "INFO: GLWorldScene: Received signal atomInserted for atom "+toString(_id)+".");
  GLMoleculeObject_atom *atomObject = new GLMoleculeObject_atom(GLMoleculeObject::meshSphere, this, _id);
  AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
  ASSERT(iter == AtomsinSceneMap.end(),
      "GLWorldScene::atomAdded() - same atom with id "+toString(_id)+" added again.");
  AtomsinSceneMap.insert( make_pair(_id, atomObject) );

  qRegisterMetaType<atomId_t>("atomId_t");
  qRegisterMetaType<bond::ptr>("bond::ptr");
  qRegisterMetaType<GLMoleculeObject_bond::SideOfBond>("GLMoleculeObject_bond::SideOfBond");
  connect (atomObject, SIGNAL(clicked(atomId_t)), this, SIGNAL(atomClicked(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 *)));
  connect (atomObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
  connect (atomObject, SIGNAL(BondsInserted(const bond::ptr , const GLMoleculeObject_bond::SideOfBond)), this, SLOT(bondInserted(const bond::ptr , const GLMoleculeObject_bond::SideOfBond)));
  connect (atomObject, SIGNAL(indexChanged(GLMoleculeObject_atom*, int, int)), this, SIGNAL(changeAtomId(GLMoleculeObject_atom*, int, int)));

  updateBoundingBox();

  //bondsChanged(_atom);
  emit changeOccured();
}

/** Removes an atom of this molecule from the scene.
 *
 * We just the id as the atom might have already been destroyed.
 *
 * @param _id id of atom to remove
 */
void GLMoleculeObject_molecule::atomRemoved(const atomicNumber_t _id)
{
  LOG(3, "INFO: GLWorldScene: Received signal atomRemoved for atom "+toString(_id)+".");
  // bonds are removed by signal coming from ~bond
  // remove atoms
  AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
  ASSERT(iter != AtomsinSceneMap.end(),
      "GLWorldScene::atomRemoved() - atom "+toString(_id)+" not on display.");
  GLMoleculeObject_atom *atomObject = iter->second;
  atomObject->disconnect();
  AtomsinSceneMap.erase(iter);
  delete atomObject;

  updateBoundingBox();

  emit changeOccured();
}

void GLMoleculeObject_molecule::hoverChangedSignalled(GLMoleculeObject *ob)
{
  // Find the atom, ob corresponds to.
  hoverAtom = NULL;
  GLMoleculeObject_atom *atomObject = dynamic_cast<GLMoleculeObject_atom *>(ob);
  if (atomObject){
    for (AtomNodeMap::iterator iter = AtomsinSceneMap.begin();iter != AtomsinSceneMap.end(); ++ iter){
      if (iter->second == atomObject)
        hoverAtom = World::getInstance().getAtom(AtomById(iter->first));
    }
  }

  // Propagate signal.
  emit hoverChanged(hoverAtom);
}


/** Helper function to get bond ids in the correct order for BondNodeMap.
 *
 * \return pair of ids in correct order.
 */
GLMoleculeObject_molecule::BondIds GLMoleculeObject_molecule::getBondIds(
    const bond::ptr _bond,
    const enum GLMoleculeObject_bond::SideOfBond _side)
{
  BondIds ids;
  switch (_side) {
    case GLMoleculeObject_bond::left:
      ids = std::make_pair(_bond->leftatom->getId(), _bond->rightatom->getId());
      break;
    case GLMoleculeObject_bond::right:
      ids = std::make_pair(_bond->rightatom->getId(), _bond->leftatom->getId());
      break;
  }
  return ids;
}

/** Adds a bond to the scene.
 *
 * @param _bond bond to add
 * @param side which side of the bond (left or right)
 */
void GLMoleculeObject_molecule::bondInserted(const bond::ptr _bond, const enum GLMoleculeObject_bond::SideOfBond _side)
{
  LOG(3, "INFO: GLWorldScene::bondInserted() - Adding bond "+toString(*_bond)+".");
  //LOG(4, "INFO: Currently present bonds " << BondsinSceneMap << ".");

  const BondIds ids = getBondIds(_bond, _side);
  BondNodeMap::iterator iter = BondsinSceneMap.find(ids);
  if (iter == BondsinSceneMap.end()) {
    GLMoleculeObject_bond * bondObject =
        new GLMoleculeObject_bond(GLMoleculeObject::meshCylinder, this, _bond, _side);
    connect (
        bondObject, SIGNAL(BondRemoved(const atomId_t, const atomId_t)),
        this, SLOT(bondRemoved(const atomId_t, const atomId_t)));
    connect (bondObject, SIGNAL(changed()), this, SIGNAL(changed()));
    BondsinSceneMap.insert( make_pair(ids, bondObject) );
  //    BondIdsinSceneMap.insert( Leftids );
  } else {
    iter->second->resetPosition();
    iter->second->resetWidth();
  }
  emit changeOccured();
}

/** Removes a bond from the scene.
 *
 * @param _bond bond to remove
 */
void GLMoleculeObject_molecule::bondRemoved(const atomId_t leftnr, const atomId_t rightnr)
{
  LOG(3, "INFO: GLWorldScene::bondRemoved() - Removing bond between "+toString(leftnr)+" and "+toString(rightnr)+".");
  {
    // left bond
    const BondIds Leftids( make_pair(leftnr, rightnr) );
    BondNodeMap::iterator leftiter = BondsinSceneMap.find( Leftids );
    ASSERT(leftiter != BondsinSceneMap.end(),
        "GLWorldScene::bondRemoved() - bond "+toString(leftnr)+"-"
        +toString(rightnr)+" not on display.");
    GLMoleculeObject_bond *bondObject = leftiter->second;
    bondObject->disconnect();
    BondsinSceneMap.erase(leftiter);
    delete bondObject; // is done by signal from bond itself
    //LOG(4, "INFO: Still present bonds " << BondsinSceneMap << ".");
  }

  emit changeOccured();
}

std::ostream &operator<<(std::ostream &ost, const GLMoleculeObject_molecule::BondIds &t)
{
  ost << t.first << "," << t.second;
  return ost;
}