rdkit/Code/GraphMol/FMCS/DuplicatedSeedCache.h

//
//  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 <map>
#include <vector>
#include <stdexcept>
#include <algorithm>

namespace RDKit {
    namespace FMCS {
        class DuplicatedSeedCache {
        public:
            typedef bool TValue;
            class TKey {
                std::vector<unsigned>   AtomIdx;    // sorted
                std::vector<unsigned>   BondIdx;    // sorted
            public:
                size_t getNumAtoms()const {
                    return AtomIdx.size();
                }
                size_t getNumBonds()const {
                    return BondIdx.size();
                }

                void addAtom(unsigned i) {
                    std::vector<unsigned>::iterator it = std::lower_bound(AtomIdx.begin(), AtomIdx.end(), i);
                    AtomIdx.insert(it, i);
                }
                void addBond(unsigned i) {
                    std::vector<unsigned>::iterator it = std::lower_bound(BondIdx.begin(), BondIdx.end(), i);
                    BondIdx.insert(it, i);
                }

                bool operator == (const TKey& right)const { //opt.
                    return AtomIdx.size() == right.AtomIdx.size()
                           && BondIdx.size() == right.BondIdx.size()
                           && 0==memcmp(&AtomIdx[0], &right.AtomIdx[0], AtomIdx.size()*sizeof(unsigned))
                           && 0==memcmp(&BondIdx[0], &right.BondIdx[0], BondIdx.size()*sizeof(unsigned));
                }

                bool operator < (const TKey& right)const {
                    if(AtomIdx.size() < right.AtomIdx.size())
                        return true;
                    if(AtomIdx.size() > right.AtomIdx.size())
                        return false;

                    if(BondIdx.size() < right.BondIdx.size())
                        return true;
                    if(BondIdx.size() > right.BondIdx.size())
                        return false;

                    // everything is equal -> perform straight comparision
                    int diff;
                    diff = memcmp(&AtomIdx[0], &right.AtomIdx[0], AtomIdx.size()*sizeof(unsigned));
                    if(diff < 0)
                        return true;
                    if(diff > 0)
                        return false;
                    return memcmp(&BondIdx[0], &right.BondIdx[0], BondIdx.size()*sizeof(unsigned)) < 0;
                }
            };
        private:
            std::map<TKey, TValue> Index;
            size_t              MaxAtoms;  // max key in the cache for fast failed find
        public:
            DuplicatedSeedCache() : MaxAtoms(0) {}
            void clear() {
                Index.clear();
                MaxAtoms=0;
            }

            bool find(const TKey& key, TValue& value)const {
                value = false;
                if(key.getNumAtoms() > MaxAtoms)
                    return false;// fast check if key greater then max key in the cache

                std::map<TKey, TValue>::const_iterator entryit = Index.find(key);
                if(Index.end() != entryit)
                    value = entryit->second;
                return Index.end() != entryit;
            }

            void add(const TKey& key, TValue found=true) {
                if(key.getNumAtoms() > MaxAtoms)
                    MaxAtoms = key.getNumAtoms();

                Index.insert( std::pair<TKey, bool>(key, found));
            }

            size_t size()const  {
                return Index.size();   // for statistics only
            }
        };

    }
}