/*
 * Fragmentation.hpp
 *
 *  Created on: Oct 18, 2011
 *      Author: heber
 */

#ifndef FRAGMENTATION_HPP_
#define FRAGMENTATION_HPP_


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

#include "Graph/DepthFirstSearchAnalysis.hpp"

#include "Fragmentation/HydrogenSaturation_enum.hpp"
#include "Fragmentation/fragmentation_helpers.hpp"
#include "types.hpp"

#include <map>
#include <string>
#include <vector>

class atom;
class AtomMask_t;
class Graph;
class KeySet;
class molecule;

class Fragmentation
{
public:
  Fragmentation(molecule *_mol, const enum HydrogenSaturation _saturation);
  ~Fragmentation();

  int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, std::string prefix, DepthFirstSearchAnalysis &DFS);

  void setOutputTypes(const std::vector<std::string> &types);

private:

  void FragmentBOSSANOVA(molecule *mol, Graph *&FragmentList, KeyStack &RootStack);
  int GuesstimateFragmentCount(int order);

  bool CreateMappingLabelsToConfigSequence(std::map<atomId_t, int> &SortIndex);

  // order at site
  bool CheckOrderAtSite(AtomMask_t &AtomMask, Graph *GlobalKeySetList, int Order, std::string path, bool LoopDoneAlready);
  bool StoreOrderAtSiteFile(std::string &path);
  bool ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, std::string &path);

  // storing fragments
  molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
  int StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList);
  void CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem);

private:
  //!> pointer to molecule that is fragmented
  molecule *mol;
  //!> whether to saturate dangling bonds with hydrogen and hence treat hydrogen special
  const enum HydrogenSaturation saturation;
  //!> list of parser types for which a configuration file per fragment is stored
  std::vector<std::string> typelist;
};


#endif /* FRAGMENTATION_HPP_ */