//
//  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.
//
#include <RDGeneral/export.h>
#include <list>
#include <algorithm>
#include <math.h>
#include "SubstructMatchCustom.h"

namespace RDKit {
namespace FMCS {
class RDKIT_FMCS_EXPORT RingMatchTableSet {
  class RingMatchTable {
    FMCS::MatchTable MatchMatrix;
    std::map<const INT_VECT*, unsigned> RingIndex;

   public:
    inline void clear() {
      MatchMatrix.clear();
      RingIndex.clear();
    }
    inline void resize(unsigned s1, unsigned s2) {
      MatchMatrix.resize(s1, s2);
      for (size_t i = 0; i < s1; i++)
        for (size_t j = 0; j < s2; j++) MatchMatrix.set(i, j, false);
    }
    inline void makeRingIndex(const ROMol* mol2) {
      unsigned i = 0;
      // for each TARGET ring
      const RingInfo::VECT_INT_VECT& rings2 = mol2->getRingInfo()->bondRings();
      for (RingInfo::VECT_INT_VECT::const_iterator r2 = rings2.begin();
           r2 != rings2.end(); r2++)
        RingIndex[&*r2] = i++;
    }
    inline bool isEqual(unsigned i, const INT_VECT* r2) const {
      return MatchMatrix.at(i, getRingIndex(r2));
    }
    inline void setMatch(unsigned i, const INT_VECT* r2) {
      MatchMatrix.set(i, getRingIndex(r2), true);
    }

   private:
    inline unsigned getRingIndex(const INT_VECT* r2) const {
      std::map<const INT_VECT*, unsigned>::const_iterator j =
          RingIndex.find(r2);
      if (RingIndex.end() == j) throw - 1;
      return j->second;
    }
  };

 private:
  std::vector<std::vector<size_t>>* QueryBondRingsIndeces;
  std::map<const ROMol*, std::vector<std::vector<size_t>>>
      TargetBondRingsIndecesSet;  // by target molecules

  std::map<const ROMol*, RingMatchTable> MatchMatrixSet;  // by target molecules
  std::map<const INT_VECT*, unsigned> QueryRingIndex;

 public:
  RingMatchTableSet() : QueryBondRingsIndeces(0) {}

  inline void clear() {
    if (QueryBondRingsIndeces) QueryBondRingsIndeces->clear();
    TargetBondRingsIndecesSet.clear();
    MatchMatrixSet.clear();
    QueryRingIndex.clear();
  }

  inline bool isQueryBondInRing(unsigned bi) const {
    return (*QueryBondRingsIndeces)[bi].empty();
  }
  inline const std::vector<size_t>& getQueryBondRings(unsigned bi) const {
    return (*QueryBondRingsIndeces)[bi];
  }

  inline bool isTargetBondInRing(const ROMol* target, unsigned bi) const {
    std::map<const ROMol*, std::vector<std::vector<size_t>>>::const_iterator i =
        TargetBondRingsIndecesSet.find(target);
    if (TargetBondRingsIndecesSet.end() == i) throw - 1;  // never
    return i->second[bi].empty();
  }
  inline const std::vector<size_t>& getTargetBondRings(const ROMol* target,
                                                       unsigned bi) const {
    std::map<const ROMol*, std::vector<std::vector<size_t>>>::const_iterator i =
        TargetBondRingsIndecesSet.find(target);
    if (TargetBondRingsIndecesSet.end() == i) throw - 1;  // never
    return i->second[bi];
  }

  inline bool isEqual(const INT_VECT* r1, const INT_VECT* r2,
                      const ROMol* mol2) const {
    const RingMatchTable& m = getTargetMatchMatrix(mol2);
    unsigned i = getQueryRingIndex(r1);
    return m.isEqual(i, r2);
  }

  void init(const ROMol* query) {
    MatchMatrixSet.clear();
    // fill out QueryRingIndex
    unsigned i = 0;
    const RingInfo::VECT_INT_VECT& rings = query->getRingInfo()->bondRings();
    for (RingInfo::VECT_INT_VECT::const_iterator r = rings.begin();
         r != rings.end(); r++)
      QueryRingIndex[&*r] = i++;
    TargetBondRingsIndecesSet.clear();
    QueryBondRingsIndeces = &TargetBondRingsIndecesSet[query];
    QueryBondRingsIndeces->resize(query->getNumBonds());
    size_t ri = 0;
    for (RingInfo::VECT_INT_VECT::const_iterator r = rings.begin();
         r != rings.end(); r++, ri++)
      for (INT_VECT::const_iterator bi = r->begin(); bi != r->end();
           bi++)  // all bonds in the ring
        (*QueryBondRingsIndeces)[*bi].push_back(ri);
  }
  inline void addTargetBondRingsIndeces(const ROMol* mol2) {
    std::vector<std::vector<size_t>>& m = TargetBondRingsIndecesSet[mol2];
    m.resize(mol2->getNumBonds());

    size_t ri = 0;
    const RingInfo::VECT_INT_VECT& rings = mol2->getRingInfo()->bondRings();
    for (RingInfo::VECT_INT_VECT::const_iterator r = rings.begin();
         r != rings.end(); r++, ri++)
      for (INT_VECT::const_iterator bi = r->begin(); bi != r->end();
           bi++)  // all bonds in the ring
        m[*bi].push_back(ri);
  }

  void computeRingMatchTable(
      const ROMol* query, const ROMol* targetMolecule,
      const MCSParameters& parameters) {  // call it for all targets
    const RingInfo::VECT_INT_VECT& rings1 = query->getRingInfo()->bondRings();
    const RingInfo::VECT_INT_VECT& rings2 =
        targetMolecule->getRingInfo()->bondRings();
    RingMatchTable& m =
        addTargetMatchMatrix(targetMolecule, rings1.size(), rings2.size());
    unsigned i = 0;
    // for each query ring
    for (RingInfo::VECT_INT_VECT::const_iterator r1 = rings1.begin();
         r1 != rings1.end(); r1++, i++) {
      FMCS::Graph graph1;
      makeRingGraph(graph1, *r1,
                    query);  // for each query ring bond ADD all atoms and bonds

      // for each TARGET ring
      for (RingInfo::VECT_INT_VECT::const_iterator r2 = rings2.begin();
           r2 != rings2.end(); r2++) {
        if (r1->size() != r2->size())  // rings are different
          continue;
        FMCS::Graph graph2;
        makeRingGraph(
            graph2, *r2,
            targetMolecule);  // for each TAG ring bond ADD all atoms and bonds

        // check ring substruct match
        MCSBondCompareParameters bp = parameters.BondCompareParameters;
        bp.RingMatchesRingOnly = false;
        bp.CompleteRingsOnly = false;
        bool match =
#ifdef NEVER_xxx_PRECOMPUTED_TABLES_MATCH  // not computed yet, because
                                           // MatchTable computation usees this
                                           // ring info table
            FMCS::SubstructMatchCustomTable(graph2, graph1, tag->AtomMatchTable,
                                            tag->BondMatchTable);
#else  // noticable slowly:
            FMCS::SubstructMatchCustom(
                graph2, *targetMolecule, graph1, *query, parameters.AtomTyper,
                parameters.BondTyper, NULL, parameters.AtomCompareParameters,
                bp, NULL);
#endif
        if (match) m.setMatch(i, &*r2);
      }
    }
  }

 private:
  void makeRingGraph(FMCS::Graph& g, const INT_VECT& ring,
                     const ROMol* mol) const {  // ADD all atoms and bonds
    std::map<const Atom*, unsigned> atomMap;

    for (size_t i = 0; i < ring.size(); i++) {
      const Bond* bond = mol->getBondWithIdx(ring[i]);
      const Atom* atom1 = bond->getBeginAtom();
      const Atom* atom2 = bond->getEndAtom();
      unsigned j1 = NotSet;
      unsigned j2 = NotSet;
      std::map<const Atom*, unsigned>::const_iterator ai;
      ai = atomMap.find(atom1);
      if (atomMap.end() != ai) j1 = ai->second;
      ai = atomMap.find(atom2);
      if (atomMap.end() != ai) j2 = ai->second;
      if (NotSet == j1) {
        j1 = g.m_vertices.size();
        atomMap[atom1] = j1;
        g.addAtom(atom1->getIdx());
      }
      if (NotSet == j2) {
        j2 = g.m_vertices.size();
        atomMap[atom2] = j2;
        g.addAtom(atom2->getIdx());
      }
      g.addBond(ring[i], j1, j2);
    }
  }

  inline unsigned getQueryRingIndex(const INT_VECT* r1) const {
    std::map<const INT_VECT*, unsigned>::const_iterator i =
        QueryRingIndex.find(r1);
    if (QueryRingIndex.end() == i) throw - 1;  // never
    return i->second;
  }
  inline const RingMatchTable& getTargetMatchMatrix(const ROMol* mol2) const {
    std::map<const ROMol*, RingMatchTable>::const_iterator mi =
        MatchMatrixSet.find(mol2);
    if (MatchMatrixSet.end() == mi) throw - 1;  // never
    return mi->second;
  }

  inline RingMatchTable& addTargetMatchMatrix(const ROMol* mol2, unsigned s1,
                                              unsigned s2) {
    RingMatchTable& m = MatchMatrixSet[mol2];
    m.resize(s1, s2);
    m.makeRingIndex(mol2);
    return m;
  }
};
}  // namespace FMCS
}  // namespace RDKit
