//
//  Copyright (C) 2014 Novartis Institutes for BioMedical Research
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#pragma once
#include <vector>
#include <string>
#include <stdexcept>
#include "../RDKitBase.h"
#include "FMCS.h"
#include "DebugTrace.h"  // algorithm filter definitions
#include "SeedSet.h"
#include "Target.h"
#include "SubstructureCache.h"
#include "DuplicatedSeedCache.h"
#include "MatchTable.h"
#include "TargetMatch.h"
#include "RingMatchTableSet.h"

namespace RDKit {

bool FinalChiralityCheckFunction(const short unsigned c1[],
                                 const short unsigned c2[], const ROMol& mol1,
                                 const FMCS::Graph& query, const ROMol& mol2,
                                 const FMCS::Graph& target,
                                 const MCSParameters* p);

namespace FMCS {
class MaximumCommonSubgraph {
  struct MCS {  // current result. Reference to a fragment of source molecule
    std::vector<const Atom*> Atoms;
    std::vector<const Bond*> Bonds;
    std::vector<unsigned> AtomsIdx;
    std::vector<unsigned> BondsIdx;  // need for results and size() only !
    const ROMol* QueryMolecule;
    std::vector<Target> Targets;
  };

  unsigned long long To;
  MCSProgressData Stat;
  MCSParameters Parameters;
  unsigned ThresholdCount;  // min number of matching
  std::vector<const ROMol*> Molecules;
#ifdef FAST_SUBSTRUCT_CACHE
  std::vector<unsigned> QueryAtomLabels;  // for code Morgan. Value based on
                                          // current functor and parameters
  std::vector<unsigned> QueryBondLabels;  // for code Morgan. Value based on
                                          // current functor and parameters
  SubstructureCache HashCache;
  MatchTable QueryAtomMatchTable;
  MatchTable QueryBondMatchTable;
  RingMatchTableSet RingMatchTables;
#endif
#ifdef DUP_SUBSTRUCT_CACHE
  DuplicatedSeedCache DuplicateCache;
#endif
  const ROMol* QueryMolecule;
  unsigned QueryMoleculeMatchedBonds;
  unsigned QueryMoleculeMatchedAtoms;
  std::vector<Target> Targets;
  SeedSet Seeds;
  MCS McsIdx;

 public:
#ifdef VERBOSE_STATISTICS_ON
  ExecStatistics VerboseStatistics;
#endif

  MaximumCommonSubgraph(const MCSParameters* params);
  ~MaximumCommonSubgraph() { clear(); }
  MCSResult find(const std::vector<ROMOL_SPTR>& mols);
  const ROMol& getQueryMolecule() const { return *QueryMolecule; }
  unsigned getMaxNumberBonds() const { return McsIdx.BondsIdx.size(); }

  unsigned getMaxNumberAtoms() const { return McsIdx.AtomsIdx.size(); }
  // internal:
  bool checkIfMatchAndAppend(Seed& seed);

 private:
  void clear() {
    Targets.clear();
    Molecules.clear();
    To = nanoClock();
  }
  void init();
  void makeInitialSeeds();
  bool createSeedFromMCS(size_t newQueryTarget, Seed& seed);
  bool growSeeds();  // returns false if canceled
  std::string generateResultSMARTS(const MCS& McsIdx) const;

  bool match(Seed& seed);
  bool matchIncrementalFast(Seed& seed, unsigned itarget);
};
}
}  // namespace RDKit
