/*
 * MoleculeLeafClass.hpp
 *
 *  Created on: Oct 20, 2011
 *      Author: heber
 */

#ifndef MOLECULELEAFCLASS_HPP_
#define MOLECULELEAFCLASS_HPP_

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

#include "Fragmentation/fragmentation_helpers.hpp"

class atom;
class Graph;
class molecule;


/** A leaf for a tree of \a molecule class
 * Wraps molecules in a tree structure
 */
class MoleculeLeafClass
{
public:
  molecule *Leaf; //!< molecule of this leaf
  //MoleculeLeafClass *UpLeaf;        //!< Leaf one level up
  //MoleculeLeafClass *DownLeaf;      //!< First leaf one level down
  MoleculeLeafClass *previous; //!< Previous leaf on this level
  MoleculeLeafClass *next; //!< Next leaf on this level

  //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
  MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
  ~MoleculeLeafClass();

  bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
  bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
  bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
  void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
  int Count() const;
};


#endif /* MOLECULELEAFCLASS_HPP_ */