/*
 * AdjacencyList.hpp
 *
 *  Created on: Mar 3, 2011
 *      Author: heber
 */

#ifndef ADJACENCYLIST_HPP_
#define ADJACENCYLIST_HPP_

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

#include <iosfwd>
#include <map>
#include <set>

#include "types.hpp"
#include "World.hpp"

class atom;

/** This class contains the adjacency structure inside an internal map of atoms.
 *
 * The adjacency structure is either from a file or from a given set of atoms.
 *
 * We may compare a subset of atoms against this internal bond structure. It is
 * true it is a true subset of the bond structure.
 */
class AdjacencyList
{
  //!> Unit test is granted access to internal data
  friend class AdjacencyListTest;
public:
  typedef std::vector<atomId_t> atomids_t;

  AdjacencyList(std::istream &File);
  AdjacencyList(const atomids_t &atoms);
  ~AdjacencyList();

  bool CheckAgainstSubset(const atomids_t &atoms);

private:
  typedef std::set<atomId_t> KeysSet;
  typedef std::set<atomId_t> ValuesSet;
  typedef std::pair<atomId_t, atomId_t> AtomBondPair;
  typedef std::multimap< atomId_t, atomId_t > AtomBondMap;
  typedef std::pair<AtomBondMap::const_iterator, AtomBondMap::const_iterator> AtomBondRange;
  AtomBondMap InternalAtomBondMap;
  AtomBondMap ExternalAtomBondMap;
  int NonMatchNumber;

  KeysSet getKeys(const AtomBondRange &_range) const;
  ValuesSet getValues(const AtomBondRange&_range) const;

  void CreateExternalMap(const atomids_t &atoms);
  bool ParseInInternalMap(std::istream &File);
  bool CompareInternalExternalMap();
};

#endif /* ADJACENCYLIST_HPP_ */