/*
 * 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/Views/Qt4/QtSelectionChangedAgent.hpp"

#include "CodePatterns/MemDebug.hpp"

#include "CodePatterns/Log.hpp"

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

#include <iostream>

using namespace MoleCuilder;

GLWorldScene::GLWorldScene(QObject *parent) :
    QObject(parent),
    selectionMode(SelectAtom)
{
  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(this, SIGNAL(moleculePreparedInserted(const moleculeId_t)), this, SLOT(moleculeInserted(const moleculeId_t)));
  connect(this, SIGNAL(moleculePreparedRemoved(const moleculeId_t)), this, SLOT(moleculeRemoved(const moleculeId_t)));

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

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

///** Update the WorldScene with molecules and atomsfrom World.
// *
// * This function should be called after e.g. WorldTime::TimeChanged was
// * received or after another molecule has been loaded.
// *
// */
//void GLWorldScene::update()
//{
//  const std::vector<const molecule *> &molecules =
//      const_cast<const World &>(World::getInstance()).getAllMolecules();
//
//  for (std::vector<const molecule*>::const_iterator moliter = molecules.begin();
//      moliter != molecules.end();
//      moliter++) {
//    // check whether molecule already exists
//    const moleculeId_t molid = (*moliter)->getId();
//    const bool mol_present = MoleculesinSceneMap.count(molid);
//    if (!mol_present)
//      moleculeInserted((*moliter)->getId());
//  }
//
//  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.begin();
//  for (;iter != MoleculesinSceneMap.end();) {
//    const moleculeId_t molid = iter->first;
//    const molecule * const mol = const_cast<const World &>(World::getInstance()).
//        getMolecule(MoleculeById(molid));
//    const bool mol_absent = (mol == NULL);
//    // step on to next molecule before possibly removing entry and invalidating iter
//    ++iter;
//    if (mol_absent)
//      moleculeRemoved(molid);
//  }
//
//}

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

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

/** Inserts an atom into the scene before molecule is present.
 *
 * @param _molid molecule to insert atom for
 * @param _atomid atom to insert
 */
void GLWorldScene::atomInserted(const moleculeId_t _molid, const atomId_t _atomid)
{
  LOG(3, "INFO: GLWorldScene: Received signal atomInserted for atom "+toString(_atomid)+".");

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

  // check of molecule is already present
  if (MoleculesinSceneMap.count(_molid) != 0) {
    // pass signal through
  } else {
    // store signal for when it is instantiated
    if (MoleculeMissedStateMap.count(_molid) == 0)
      MoleculeMissedStateMap.insert( std::make_pair(_molid ,StateChangeMap_t()) );
    MoleculeMissedStateMap[_molid].insert( std::make_pair(_atomid, atomInsertedState) );
  }
}

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

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

  // check of molecule is already present
  if (MoleculesinSceneMap.count(_molid) != 0) {
    // pass signal through
  } else {
    // store signal for when it is instantiated
    if (MoleculeMissedStateMap.count(_molid) == 0)
      MoleculeMissedStateMap.insert( std::make_pair(_molid ,StateChangeMap_t()) );
    MoleculeMissedStateMap[_molid].insert( std::make_pair(_atomid, atomRemovedState) );
  }
}

/** Prepres insertion of a molecule into the scene.
 *
 * This function takes up the insertion information, i.e. a molecule has been
 * inserted and its id, and takes some immediate action (writing id into a map).
 * But the request is then transmitted indirectly (i.e. not necessarily being
 * processed in the same thread). Hence, we first take the request via a direction
 * connection in the thread where the actual World::createMolecule() was called.
 * However, the creation of the visual representation must occur in the thread
 * who also contains GLWorldScene and GLWorldView and all further parents.
 *
 * That's the reason why we split here into moleculePrepareInserted and
 * moleculeInserted.
 *
 * @param _mol molecule to insert
 */
void GLWorldScene::moleculePrepareInserted(const moleculeId_t _id)
{
  LOG(3, "INFO: GLWorldScene: Received signal moleculePrepareInserted for molecule "+toString(_id)+".");

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

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

  emit moleculePreparedInserted(_id);
}

/** Inserts a molecule into the scene.
 *
 * \sa moleculePrepareInserted()
 *
 * @param _mol molecule to insert
 */
void GLWorldScene::moleculeInserted(const moleculeId_t _id)
{
  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);

  // check whether molecule is still present
  if (RemovalMolecules.count(_id) != 0) {
    RemovalMolecules.erase(_id);
    return;
  }
  if (const_cast<const World &>(World::getInstance()).getMolecule(MoleculeById(_id)) == NULL) {
    ELOG(2, "Molecule with id " << _id << " has disappeared.");
    return;
  }

  // add new object
  GLMoleculeObject_molecule *molObject =
      new GLMoleculeObject_molecule(GLMoleculeObject::meshEmpty, this, _id);
  ASSERT( molObject != NULL,
      "GLWorldScene::moleculeInserted - could not create molecule object for "+toString(_id));
  MoleculesinSceneMap.insert( make_pair(_id, molObject) );

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

  // now let the molObject sign on to molecule
  molObject->activateObserver();

  connect (molObject, SIGNAL(changed()), this, SIGNAL(changed()));
  connect (molObject, SIGNAL(changeOccured()), this, SIGNAL(changeOccured()));
  connect (molObject, SIGNAL(atomClicked(atomId_t)), this, SLOT(atomClicked(atomId_t)));
  connect (molObject, SIGNAL(moleculeClicked(moleculeId_t)), this, SLOT(moleculeClicked(moleculeId_t)));
  connect (molObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
  connect (molObject, SIGNAL(selectionChanged()), this, SIGNAL(changed()));
  connect (molObject, SIGNAL(hoverChanged(const atomId_t)), this, SIGNAL(hoverChanged(const atomId_t)));
  connect (molObject, SIGNAL(hoverChanged(const moleculeId_t, int)), this, SIGNAL(hoverChanged(const moleculeId_t, int)));
  connect (molObject, SIGNAL(indexChanged(GLMoleculeObject_molecule *, const moleculeId_t, const moleculeId_t)), this, SLOT(changeMoleculeId(GLMoleculeObject_molecule *, const moleculeId_t, const moleculeId_t)));

  emit changed();
  emit changeOccured();
}

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

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

  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_id);
  if ( iter == MoleculesinSceneMap.end())
    RemovalMolecules.insert(_id);

  emit moleculePreparedRemoved(_id);
}

/** Removes a molecule from the scene.
 *
 * * \sa moleculePrepareRemoved()
 *
 * @param _id id of molecule to remove
 */
void GLWorldScene::moleculeRemoved(const moleculeId_t _id)
{
  boost::recursive_mutex::scoped_lock lock(MoleculeinSceneMap_mutex);

  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_id);
  GLMoleculeObject_molecule *molObject = iter->second;
  molObject->disconnect();
  MoleculesinSceneMap.erase(iter);
  delete molObject;

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

  emit changed();
  emit changeOccured();
}

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

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

  emit changed();
  emit changeOccured();
}

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

  emit changed();
}

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

  emit changed();
}

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

  emit changed();
}

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

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

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

void GLWorldScene::setSelectionChangedAgent(QtSelectionChangedAgent *agent)
{
  connect(agent, SIGNAL(atomSelected(const moleculeId_t, const atomId_t)),
      this, SLOT(AtomSelected(const moleculeId_t, const atomId_t)));
  connect(agent, SIGNAL(atomUnselected(const moleculeId_t, const atomId_t)),
      this, SLOT(AtomUnselected(const moleculeId_t, const atomId_t)));

  connect(agent, SIGNAL(moleculeSelected(const moleculeId_t)),
      this, SLOT(MoleculeSelected(const moleculeId_t)));
  connect(agent, SIGNAL(moleculeUnselected(const moleculeId_t)),
      this, SLOT(MoleculeUnselected(const moleculeId_t)));
}

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

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

void GLWorldScene::changeMoleculeId(
    GLMoleculeObject_molecule *ob,
    const moleculeId_t oldId,
    const moleculeId_t newId)
{
  LOG(3, "INFO: GLWorldScene - change molecule id " << oldId << " to " << newId << ".");

  {
    // Remove from map.
    MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(oldId);
    ASSERT(iter != MoleculesinSceneMap.end(),
        "GLWorldScene::changeMoleculeId() - molecule with old id "+toString(oldId)+" not on display.");
    ASSERT(iter->second == ob,
        "GLWorldScene::changeMoleculeId() - molecule with id "
        +toString(oldId)+" does not match with object in MoleculesinSceneMap.");
    MoleculesinSceneMap.erase(iter);

    // Reinsert with new id.
    {
      MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(newId);
      ASSERT(iter == MoleculesinSceneMap.end(),
            "GLWorldScene::changeMoleculeId() -  moleculewith new id "+toString(newId)+" already known.");
    }
    MoleculesinSceneMap.insert( make_pair(newId, ob) );
  }

  {
    // Remove and re-insert from map if present.
    MoleculeMissedStateMap_t::iterator iter = MoleculeMissedStateMap.find(oldId);
    if (iter != MoleculeMissedStateMap.end()) {
      StateChangeMap_t changemap = iter->second;
      MoleculeMissedStateMap.erase(iter);
      MoleculeMissedStateMap.insert( std::make_pair(newId, changemap) );
    }
  }
}

void GLWorldScene::AtomSelected(const moleculeId_t _molid, const atomId_t _id)
{
  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_molid);
  if (iter != MoleculesinSceneMap.end())
    QMetaObject::invokeMethod(iter->second,        // pointer to a QObject
                            "AtomSelected",       // member name (no parameters here)
                            Qt::QueuedConnection,     // connection type
                            Q_ARG(const atomId_t, _id));     // parameters
  else
    ELOG(2, "DEBUG: GLWorldScene::AtomSelected() - molecule " <<
        _molid << " unknown to GLWorldScene.");
}

void GLWorldScene::AtomUnselected(const moleculeId_t _molid, const atomId_t _id)
{
  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_molid);
  if (iter != MoleculesinSceneMap.end())
    QMetaObject::invokeMethod(iter->second,        // pointer to a QObject
                            "AtomUnselected",       // member name (no parameters here)
                            Qt::QueuedConnection,     // connection type
                            Q_ARG(const atomId_t, _id));     // parameters
  else
    ELOG(2, "GLWorldScene::AtomUnselected() - molecule "
        << _molid << " unknown to GLWorldScene.");
}

void GLWorldScene::MoleculeSelected(const moleculeId_t _molid)
{
  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_molid);
  if (iter != MoleculesinSceneMap.end())
    QMetaObject::invokeMethod(iter->second,        // pointer to a QObject
                            "Selected",       // member name (no parameters here)
                            Qt::QueuedConnection);     // connection type
  else
    ELOG(2, "GLWorldScene::MoleculeSelected() - molecule "
        << _molid << " unknown to GLWorldScene.");
}

void GLWorldScene::MoleculeUnselected(const moleculeId_t _molid)
{
  MoleculeNodeMap::iterator iter = MoleculesinSceneMap.find(_molid);
  if (iter != MoleculesinSceneMap.end())
    QMetaObject::invokeMethod(iter->second,        // pointer to a QObject
                            "Unselected",       // member name (no parameters here)
                            Qt::QueuedConnection);     // connection type
  else
    ELOG(2, "GLWorldScene::MoleculeUnselected() - molecule "
        << _molid << " unknown to GLWorldScene.");
}