source: src/World.hpp@ 4464ef

/*
 * World.hpp
 *
 *  Created on: Feb 3, 2010
 *      Author: crueger
 */

#ifndef WORLD_HPP_
#define WORLD_HPP_

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

/*********************************************** includes ***********************************/

#include <string>
#include <map>
#include <vector>
#include <set>
#include <stack>
#include <boost/thread.hpp>
#include <boost/shared_ptr.hpp>

#include "Actions/ActionTrait.hpp"
#include "Atom/AtomSet.hpp"
#include "Descriptors/SelectiveConstIterator.hpp"
#include "Descriptors/SelectiveIterator.hpp"
#include "CodePatterns/Observer/Observable.hpp"
#include "CodePatterns/Observer/Observer.hpp"
#include "CodePatterns/Cacheable.hpp"
#include "CodePatterns/Singleton.hpp"
#include "CodePatterns/Observer/ObservedContainer.hpp"
#include "CodePatterns/Range.hpp"
#include "IdPool_policy.hpp"
#include "IdPool.hpp"
#include "LinkedCell/LinkedCell_View.hpp"
#include "types.hpp"


// forward declarations
class atom;
class AtomDescriptor;
class AtomDescriptor_impl;
class BondGraph;
class Box;
class config;
class HomologyContainer;
class RealSpaceMatrix;
class molecule;
class MoleculeDescriptor;
class MoleculeDescriptor_impl;
class periodentafel;
class ThermoStatContainer;

namespace LinkedCell {
  class LinkedCell_Controller;
}

namespace MoleCuilder {
  class ManipulateAtomsProcess;
  template<typename T> class AtomsCalculation;
}

/****************************************** forward declarations *****************************/

/********************************************** Class World *******************************/

namespace detail {
  template <class T> const T* lastChanged()
  {
    ASSERT(0, "detail::lastChanged() - only specializations may be used.");
    return NULL;
  }
}

class World : public Singleton<World>, public Observable
{

// Make access to constructor and destructor possible from inside the singleton
friend class Singleton<World>;

// necessary for coupling with descriptors
friend class AtomDescriptor_impl;
friend class AtomDescriptor;
friend class MoleculeDescriptor_impl;
friend class MoleculeDescriptor;
// coupling with descriptors over selection
friend class AtomSelectionDescriptor_impl;
friend class AtomOfMoleculeSelectionDescriptor_impl;
friend class AtomOrderDescriptor_impl;
friend class MoleculeOfAtomSelectionDescriptor_impl;
friend class MoleculeOrderDescriptor_impl;
friend class MoleculeSelectionDescriptor_impl;

// Actions, calculations etc associated with the World
friend class MoleCuilder::ManipulateAtomsProcess;
template<typename> friend class MoleCuilder::AtomsCalculation;
public:
  // some typedefs for the CONSTRUCT_... macros (no "," allows in a single parameter name)
  typedef std::map<atomId_t,atom*> AtomSTLSet;
  typedef std::map<moleculeId_t,molecule*> MoleculeSTLSet;

  // Types for Atom and Molecule structures
  typedef ObservedContainer< AtomSTLSet, UnobservedIterator<AtomSTLSet> > AtomSet;
  typedef ObservedContainer< MoleculeSTLSet, UnobservedIterator<MoleculeSTLSet> > MoleculeSet;

  typedef ATOMSET(std::vector) AtomComposite;
  typedef CONSTATOMSET(std::vector) ConstAtomComposite;

    /******* Notifications *******/

  //!> enumeration of present notification types: only insertion/removal of atoms or molecules
  enum NotificationType {
    AtomInserted,
    AtomRemoved,
    MoleculeInserted,
    MoleculeRemoved,
    SelectionChanged,
    NotificationType_MAX
  };

  //>! access to last changed element (atom or molecule)
  template <class T> const T* lastChanged() const
  { return detail::lastChanged<T>(); }

  const atomId_t lastChangedAtomId() const
  { return _lastchangedatomid; }

  const moleculeId_t lastChangedMolId() const
  { return _lastchangedmolid; }

    /***** getter and setter *****/
  // reference to pointer is used for legacy reason... reference will be removed latter to keep encapsulation of World object
  /**
   * returns the periodentafel for the world.
   */
  periodentafel *&getPeriode();

  /** Returns the BondGraph for the World.
   *
   * @return reference to BondGraph
   */
  BondGraph *&getBondGraph();

  /** Sets the World's BondGraph.
   *
   * @param _BG new BondGraph
   */
  void setBondGraph(BondGraph *_BG);

  /** Getter for homology container.
   *
   * \return const reference to homology container.
   */
  HomologyContainer &getHomologies();

  /** Setter for homology container.
   *
   * \param homologies reference to homologies, set to NULL
   */
  void resetHomologies(HomologyContainer *&homologies);

  /**
   * returns the configuration for the world.
   */
  config *&getConfig();

  /** Returns a notification_ptr for a specific type.
   *
   * @param type request type
   * @return reference to instance
   */
  Notification_ptr getNotification(enum NotificationType type) const;

  /**
   * returns the first atom that matches a given descriptor.
   * Do not rely on ordering for descriptors that match more than one atom.
   */
  atom* getAtom(AtomDescriptor descriptor);

  /**
   * returns the first atom that matches a given descriptor.
   * Do not rely on ordering for descriptors that match more than one atom.
   */
  const atom* getAtom(AtomDescriptor descriptor) const;

  /**
   * returns a vector containing all atoms that match a given descriptor
   */
  AtomComposite getAllAtoms(AtomDescriptor descriptor);

  /**
   * returns a vector containing all atoms that match a given descriptor
   */
  ConstAtomComposite getAllAtoms(AtomDescriptor descriptor) const;

  /**
   * returns a vector containing all atoms that match a given descriptor
   */
  AtomComposite getAllAtoms();

  /**
   * returns a vector containing all atoms that match a given descriptor
   */
  ConstAtomComposite getAllAtoms() const;

  /**
   * returns a calculation that calls a given function on all atoms matching a descriptor.
   * the calculation is not called at this point and can be used as an action, i.e. be stored in
   * menus, be kept around for later use etc.
   */
  template<typename T> MoleCuilder::AtomsCalculation<T>* calcOnAtoms(boost::function<T(atom*)>,const MoleCuilder::ActionTrait &_trait,AtomDescriptor);
  template<typename T> MoleCuilder::AtomsCalculation<T>* calcOnAtoms(boost::function<T(atom*)>,const MoleCuilder::ActionTrait &_trait);

  /**
   * get the number of atoms in the World
   */
  int numAtoms() const;

  /**
   * returns the first molecule that matches a given descriptor.
   * Do not rely on ordering for descriptors that match more than one molecule.
   */
  molecule *getMolecule(MoleculeDescriptor descriptor);

  /**
   * returns the first molecule that matches a given descriptor.
   * Do not rely on ordering for descriptors that match more than one molecule.
   */
  const molecule *getMolecule(MoleculeDescriptor descriptor) const;

  /**
   * returns a vector containing all molecules that match a given descriptor
   */
  std::vector<molecule*> getAllMolecules(MoleculeDescriptor descriptor);

  /**
   * returns a vector containing all molecules that match a given descriptor
   */
  std::vector<const molecule*> getAllMolecules(MoleculeDescriptor descriptor) const;

  /**
   * returns a vector containing all molecules that match a given descriptor
   */
  std::vector<molecule*> getAllMolecules();
  /**
   * returns a vector containing all molecules that match a given descriptor
   */
  std::vector<const molecule*> getAllMolecules() const;

  /**
   * get the number of molecules in the World
   */
  int numMolecules() const;

  /**
   * get the domain size as a symmetric matrix (6 components)
   */
  Box& getDomain();

  /**
   * Set the domain size from a matrix object
   *
   * Matrix needs to be symmetric
   */
  void setDomain(const RealSpaceMatrix &mat);

  /**
   * set the domain size as a symmetric matrix (6 components)
   */
  void setDomain(double * matrix);

  /** Returns a LinkedCell structure for obtaining neighbors quickly.
   *
   * @param distance desired linked cell edge length
   * @return view of restricted underlying LinkedCell_Model
   */
  LinkedCell::LinkedCell_View getLinkedCell(const double distance);

  /**
   * set the current time of the world.
   *
   * @param _step time step to set to
   */
  void setTime(const unsigned int _step);

  /**
   * get the current time of the world.
   *
   * @return current time step
   */
  const unsigned getTime() const;

  /**
   * get the default name
   */
  std::string getDefaultName();

  /**
   * set the default name
   */
  void setDefaultName(std::string name);

  /**
   * get pointer to World's ThermoStatContainer
   */
  ThermoStatContainer * getThermostats();

  /*
   * get the ExitFlag
   */
  int getExitFlag();

  /*
   * set the ExitFlag
   */
  void setExitFlag(int flag);

  /***** Methods to work with the World *****/

  /**
   * create a new molecule. This method should be used whenever any kind of molecule is needed. Assigns a unique
   * ID to the molecule and stores it in the World for later retrieval. Do not create molecules directly.
   */
  molecule *createMolecule();

  /**
   * Recreate a destroyed molecule.
   * This method assigns the molecule the specified \a _id. It returns NULL of the
   * id could not be assigned.
   */
  molecule *recreateMolecule(const moleculeId_t &_id);

  void destroyMolecule(molecule*);
  void destroyMolecule(moleculeId_t);

  /**
   * Create a new atom. This method should be used whenever any atom is needed. Assigns a unique ID and stores
   * the atom in the World. If the atom is not destroyed it will automatically be destroyed when the world ends.
   */
  atom *createAtom();

  /**
   * Recreate an atom after it was destroyed.
   * This method assigns the atom the specified \a _id. It returns NULL of the
   * id could not be assigned.
   */
  atom *recreateAtom(const atomId_t _id);

  /**
   * Registers a Atom unknown to world. Needed in some rare cases, e.g. when cloning atoms, or in some unittests.
   * Do not re-register Atoms already known to the world since this will cause double-frees.
   */
  int registerAtom(atom*);

  /**
     * Delete some atom and erase it from the world. Use this whenever you need to destroy any atom. Do not call delete on
     * atom directly since this will leave the pointer inside the world.
   */
  void destroyAtom(atom*);

  /**
   * Delete some atom and erase it from the world. Use this whenever you need to destroy any atom. Do not call delete on
   * atom directly since this will leave the pointer inside the world.
   */
  void destroyAtom(atomId_t);

  /**
   * used when changing an atom Id.
   * Unless you are calling this method from inside an atom don't fiddle with the third parameter.
   *
   * Return value indicates whether the change could be done or not.
   */
  bool changeAtomId(atomId_t oldId, atomId_t newId, atom* target=0);

  /**
   * used when changing an molecule Id.
   * Unless you are calling this method from inside an molecule don't fiddle with the third parameter.
   *
   * Return value indicates whether the change could be done or not.
   */
  bool changeMoleculeId(moleculeId_t oldId, moleculeId_t newId, molecule* target=0);

  /**
   * Produces a process that calls a function on all Atoms matching a given descriptor. The process is not
   * called at this time, so it can be passed around, stored inside menuItems etc.
   */
  MoleCuilder::ManipulateAtomsProcess* manipulateAtoms(boost::function<void(atom*)>,std::string,AtomDescriptor);
  MoleCuilder::ManipulateAtomsProcess* manipulateAtoms(boost::function<void(atom*)>,std::string);

  /****
   * Iterators to use internal data structures
   * All these iterators are observed to track changes.
   * There is a corresponding protected section with unobserved iterators,
   * which can be used internally when the extra speed is needed
   */

  typedef SelectiveIterator<atom*,AtomSet,AtomDescriptor>       AtomIterator;
  typedef SelectiveConstIterator<atom*,AtomSet,AtomDescriptor>       AtomConstIterator;

  /**
   * returns an iterator over all Atoms matching a given descriptor.
   * This iterator is observed, so don't keep it around unnecessary to
   * avoid unintended blocking.
   */
  AtomIterator getAtomIter(AtomDescriptor descr);
  AtomConstIterator getAtomIter(AtomDescriptor descr) const;
  AtomIterator getAtomIter();
  AtomConstIterator getAtomIter() const;

  AtomIterator atomEnd();
  AtomConstIterator atomEnd() const;

  typedef SelectiveIterator<molecule*,MoleculeSet,MoleculeDescriptor>   MoleculeIterator;
  typedef SelectiveConstIterator<molecule*,MoleculeSet,MoleculeDescriptor>   MoleculeConstIterator;

  /**
   * returns an iterator over all Molecules matching a given descriptor.
   * This iterator is observed, so don't keep it around unnecessary to
   * avoid unintended blocking.
   */
  MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
  MoleculeConstIterator getMoleculeIter(MoleculeDescriptor descr) const;
  MoleculeIterator getMoleculeIter();
  MoleculeConstIterator getMoleculeIter() const;

  MoleculeIterator moleculeEnd();
  MoleculeConstIterator moleculeEnd() const;

  /******** Selections of molecules and Atoms *************/
  void clearAtomSelection();
  void invertAtomSelection();
  void popAtomSelection();
  void pushAtomSelection();
  void selectAtom(const atom*);
  void selectAtom(const atomId_t);
  void selectAllAtoms(AtomDescriptor);
  void selectAtomsOfMolecule(const molecule*);
  void selectAtomsOfMolecule(const moleculeId_t);
  void unselectAtom(const atom*);
  void unselectAtom(const atomId_t);
  void unselectAllAtoms(AtomDescriptor);
  void unselectAtomsOfMolecule(const molecule*);
  void unselectAtomsOfMolecule(const moleculeId_t);
  size_t countSelectedAtoms() const;
  bool isSelected(const atom *_atom) const;
  bool isAtomSelected(const atomId_t no) const;
  std::vector<atom *> getSelectedAtoms();
  std::vector<const atom *> getSelectedAtoms() const;
  std::vector<atomId_t> getSelectedAtomIds() const;

  void clearMoleculeSelection();
  void invertMoleculeSelection();
  void popMoleculeSelection();
  void pushMoleculeSelection();
  void selectMolecule(const molecule*);
  void selectMolecule(const moleculeId_t);
  void selectAllMolecules(MoleculeDescriptor);
  void selectMoleculeOfAtom(const atom*);
  void selectMoleculeOfAtom(const atomId_t);
  void unselectMolecule(const molecule*);
  void unselectMolecule(const moleculeId_t);
  void unselectAllMolecules(MoleculeDescriptor);
  void unselectMoleculeOfAtom(const atom*);
  void unselectMoleculeOfAtom(const atomId_t);
  size_t countSelectedMolecules() const;
  bool isSelected(const molecule *_mol) const;
  bool isMoleculeSelected(const moleculeId_t no) const;
  std::vector<molecule *> getSelectedMolecules();
  std::vector<const molecule *> getSelectedMolecules() const;
  std::vector<moleculeId_t> getSelectedMoleculeIds() const;

  /******************** Iterators to selections *****************/
  typedef AtomSet::iterator AtomSelectionIterator;
  AtomSelectionIterator beginAtomSelection();
  AtomSelectionIterator endAtomSelection();
  typedef AtomSet::const_iterator AtomSelectionConstIterator;
  AtomSelectionConstIterator beginAtomSelection() const;
  AtomSelectionConstIterator endAtomSelection() const;

  typedef MoleculeSet::iterator MoleculeSelectionIterator;
  MoleculeSelectionIterator beginMoleculeSelection();
  MoleculeSelectionIterator endMoleculeSelection();
  typedef MoleculeSet::const_iterator MoleculeSelectionConstIterator;
  MoleculeSelectionConstIterator beginMoleculeSelection() const;
  MoleculeSelectionConstIterator endMoleculeSelection() const;

protected:
  /****
   * Iterators to use internal data structures
   * All these iterators are unobserved for speed reasons.
   * There is a corresponding public section to these methods,
   * which produce observed iterators.*/

  // Atoms
  typedef SelectiveIterator<atom*,AtomSet::set_t,AtomDescriptor>        internal_AtomIterator;

  /**
   * returns an iterator over all Atoms matching a given descriptor.
   * used for internal purposes, like AtomProcesses and AtomCalculations.
   */
  internal_AtomIterator getAtomIter_internal(AtomDescriptor descr);

  /**
   * returns an iterator to the end of the AtomSet. Due to overloading this iterator
   * can be compared to iterators produced by getAtomIter (see the mis-matching types).
   * Thus it can be used to detect when such an iterator is at the end of the list.
   * used for internal purposes, like AtomProcesses and AtomCalculations.
   */
  internal_AtomIterator atomEnd_internal();

  // Molecules
  typedef SelectiveIterator<molecule*,MoleculeSet::set_t,MoleculeDescriptor>   internal_MoleculeIterator;


  /**
   * returns an iterator over all Molecules matching a given descriptor.
   * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
   */
  internal_MoleculeIterator getMoleculeIter_internal(MoleculeDescriptor descr);

  /**
   * returns an iterator to the end of the MoleculeSet. Due to overloading this iterator
   * can be compared to iterators produced by getMoleculeIter (see the mis-matching types).
   * Thus it can be used to detect when such an iterator is at the end of the list.
   * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
   */
  internal_MoleculeIterator moleculeEnd_internal();


  /******* Internal manipulation routines for double callback and Observer mechanism ******/
  void doManipulate(MoleCuilder::ManipulateAtomsProcess *);

private:
  /** Helper to access atom::select() and molecule::select() only by type.
   *
   */
  template <class T>
  static void selectInstance(T _instance)
  { _instance->select(); }

  /** Helper to access atom::unselect() and molecule::unselect() only by type.
   *
   */
  template <class T>
  static void unselectInstance(T _instance)
  { _instance->unselect(); }

  /** Forward declaration of a helper function for selecting a vector of instances.
   *
   * \note only implemented inside World.
   *
   */
  template <class T>
  void selectVectorOfInstances(const typename T::iterator _begin, const typename T::iterator _end);

  /** Forward declaration of a helper function for unselecting a vector of instances.
   *
   * \note only implemented inside World.
   *
   */
  template <class T>
  void unselectVectorOfInstances(const typename T::iterator _begin, const typename T::iterator _end);

private:

  friend const atom *detail::lastChanged<atom>();
  friend const molecule *detail::lastChanged<molecule>();
  static atom *_lastchangedatom;
  static atomId_t _lastchangedatomid;
  static molecule*_lastchangedmol;
  static moleculeId_t _lastchangedmolid;

  BondGraph *BG;
  periodentafel *periode;
  config *configuration;
  HomologyContainer *homologies;
  Box *cell_size;
  LinkedCell::LinkedCell_Controller *LCcontroller;
  std::string defaultName;
  class ThermoStatContainer *Thermostats;
  int ExitFlag;
private:

  AtomSet atoms;
  AtomSet selectedAtoms;
  typedef std::vector<atomId_t> atomIdsVector_t;
  std::stack<atomIdsVector_t> selectedAtoms_Stack;
  /**
   * stores the pool for all available AtomIds below currAtomId
   *
   * The pool contains ranges of free ids in the form [bottom,top).
   */
  IdPool<atomId_t, uniqueId> atomIdPool;

  MoleculeSet molecules;
  MoleculeSet selectedMolecules;
  typedef std::vector<moleculeId_t> moleculeIdsVector_t;
  std::stack<moleculeIdsVector_t> selectedMolecules_Stack;
  /**
   * stores the pool for all available AtomIds below currAtomId
   *
   * The pool contains ranges of free ids in the form [bottom,top).
   */
  IdPool<moleculeId_t, continuousId> moleculeIdPool;

private:
  /**
   * private constructor to ensure creation of the world using
   * the singleton pattern.
   */
  World();

  /**
   * private destructor to ensure destruction of the world using the
   * singleton pattern.
   */
  virtual ~World();

};

/** Externalized stuff as member functions cannot be specialized without
 *  specializing the class, too.
 */
namespace detail {
  template <>       inline  const atom* lastChanged<atom>() { return World::_lastchangedatom; }
  template <>       inline  const molecule* lastChanged<molecule>() { return World::_lastchangedmol; }
}


#endif /* WORLD_HPP_ */