DuplicatedSeedCache.h
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//
// 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>
#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
}
};
} // namespace FMCS
} // namespace RDKit
RDKit::FMCS::DuplicatedSeedCache::TKey::operator==
bool operator==(const TKey &right) const
Definition: DuplicatedSeedCache.h:40
RDKit::FMCS::DuplicatedSeedCache::TKey::getNumAtoms
size_t getNumAtoms() const
Definition: DuplicatedSeedCache.h:26
RDKit::FMCS::DuplicatedSeedCache::TKey::operator<
bool operator<(const TKey &right) const
Definition: DuplicatedSeedCache.h:49
RDKit::FMCS::DuplicatedSeedCache::TKey::addAtom
void addAtom(unsigned i)
Definition: DuplicatedSeedCache.h:29
RDKit::FMCS::DuplicatedSeedCache::TKey::addBond
void addBond(unsigned i)
Definition: DuplicatedSeedCache.h:34
RDKit::FMCS::DuplicatedSeedCache::find
bool find(const TKey &key, TValue &value) const
Definition: DuplicatedSeedCache.h:77
RDKit::FMCS::DuplicatedSeedCache::TKey
Definition: DuplicatedSeedCache.h:22
RDKit::FMCS::DuplicatedSeedCache
Definition: DuplicatedSeedCache.h:19
RDKit::FMCS::DuplicatedSeedCache::size
size_t size() const
Definition: DuplicatedSeedCache.h:93
RDKit::FMCS::DuplicatedSeedCache::add
void add(const TKey &key, TValue found=true)
Definition: DuplicatedSeedCache.h:87
RDKit::FMCS::DuplicatedSeedCache::DuplicatedSeedCache
DuplicatedSeedCache()
Definition: DuplicatedSeedCache.h:71
RDKit::FMCS::DuplicatedSeedCache::clear
void clear()
Definition: DuplicatedSeedCache.h:72
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::FMCS::DuplicatedSeedCache::TValue
bool TValue
Definition: DuplicatedSeedCache.h:21
RDKit::FMCS::DuplicatedSeedCache::TKey::getNumBonds
size_t getNumBonds() const
Definition: DuplicatedSeedCache.h:27
export.h