void RingoFastIndex::_match (OracleEnv &env, int idx)
{
_last_id = idx;
BingoStorage &storage = this->_context.context().context().storage;
QS_DEF(Array<char>, stored);
storage.get(idx, stored);
if (stored[0] != 0)
return; // reaction was removed from index
BufferScanner scanner(stored);
scanner.skip(1); // skip the deletion mark
scanner.skip(scanner.readByte()); // skip the compessed rowid
profTimerStart(tall, "match");
bool res = _context.substructure.matchBinary(scanner);
profTimerStop(tall);
if (res)
{
OraRowidText & rid = matched.at(matched.add());
_decompressRowid(stored, rid);
profIncTimer("match.found", profTimerGetTime(tall));
_matched++;
}
else
{
profIncTimer("match.not_found", profTimerGetTime(tall));
_unmatched++;
}
}
bool RingoFastIndex::getLastRowid (OraRowidText &id)
{
if (_last_id < 0)
return false;
BingoStorage &storage = this->_context.context().context().storage;
QS_DEF(Array<char>, stored);
storage.get(_last_id, stored);
_decompressRowid(stored, id);
return true;
}
void MangoFastIndex::_match (OracleEnv &env, int idx)
{
_last_id = idx;
BingoStorage &storage = this->_context.context().context().storage;
QS_DEF(Array<char>, stored);
storage.get(idx, stored);
if (stored[0] != 0)
return; // molecule was removed from index
BufferScanner scanner(stored);
scanner.skip(1); // skip the deletion mark
scanner.skip(scanner.readByte()); // skip the compessed rowid
scanner.skip(2); // skip 'ord' bits count
bool res = false;
profTimerStart(tall, "match");
if (_fetch_type == _SUBSTRUCTURE)
{
QS_DEF(Array<char>, xyz_buf);
if (_context.substructure.needCoords())
{
OraRowidText rid;
_decompressRowid(stored, rid);
if (_loadCoords(env, rid.ptr(), xyz_buf))
{
BufferScanner xyz_scanner(xyz_buf);
res = _context.substructure.matchBinary(scanner, &xyz_scanner);
}
else
// no XYZ --> skip the molecule
res = false;
}
else
res = _context.substructure.matchBinary(scanner, 0);
}
else if (_fetch_type == _TAUTOMER_SUBSTRUCTURE)
res = _context.tautomer.matchBinary(scanner);
else // _fetch_type == _SIMILARITY
res = _context.similarity.matchBinary(scanner);
profTimerStop(tall);
if (res)
{
OraRowidText & rid = matched.at(matched.add());
_decompressRowid(stored, rid);
profIncTimer("match.found", profTimerGetTime(tall));
_matched++;
}
else
{
profIncTimer("match.not_found", profTimerGetTime(tall));
_unmatched++;
}
}
void MangoFastIndex::_fetchSimilarity (OracleEnv &env, int max_matches)
{
BingoFingerprints &fingerprints = _context.context().fingerprints;
int i;
if (!fingerprints.ableToScreen(_screening))
{
env.dbgPrintfTS("no bits in query fingerprint, can not do similarity search\n");
return;
}
profTimerStart(tsimfetch, "sim.fetch");
while (matched.size() < max_matches)
{
if (!fingerprints.countOnes_Init(env, _screening))
{
env.dbgPrintfTS("screening ended\n");
break;
}
BingoStorage &storage = _context.context().context().storage;
QS_DEF(Array<int>, max_common_ones);
QS_DEF(Array<int>, min_common_ones);
QS_DEF(Array<int>, target_ones);
QS_DEF(Array<char>, stored);
max_common_ones.clear_resize(_screening.block->used);
min_common_ones.clear_resize(_screening.block->used);
target_ones.clear_resize(_screening.block->used);
for (i = 0; i < _screening.block->used; i++)
{
storage.get(fingerprints.getStorageIndex_NoMap(_screening, i), stored);
BufferScanner scanner(stored);
scanner.skip(1); // skip the deletion mark
scanner.skip(scanner.readByte()); // skip the compessed rowid
target_ones[i] = scanner.readBinaryWord();
max_common_ones[i] = _context.similarity.getUpperBound(target_ones[i]);
min_common_ones[i] = _context.similarity.getLowerBound(target_ones[i]);
}
bool first = true;
bool entire = false;
_screening.passed.clear();
while (true)
{
if (!fingerprints.countOnes_Next(env, _screening))
{
env.dbgPrintf("read all %d bits, writing %d results... ",
_screening.query_ones.size(), _screening.passed.size());
entire = true;
break;
}
if (first)
{
first = false;
for (i = 0; i < _screening.block->used; i++)
{
int min_possible_ones = _screening.one_counters[i];
int max_possible_ones = _screening.one_counters[i] +
_screening.query_ones.size() - _screening.query_bit_idx;
if (min_possible_ones <= max_common_ones[i] &&
max_possible_ones >= min_common_ones[i])
_screening.passed.add(i);
}
}
else
{
int j;
for (j = _screening.passed.begin(); j != _screening.passed.end(); )
{
i = _screening.passed[j];
int min_possible_ones = _screening.one_counters[i];
int max_possible_ones = _screening.one_counters[i] +
_screening.query_ones.size() - _screening.query_bit_idx;
int next_j = _screening.passed.next(j);
if (min_possible_ones > max_common_ones[i] ||
max_possible_ones < min_common_ones[i])
_screening.passed.remove(j);
j = next_j;
}
}
if (_screening.passed.size() <= _context.context().context().sim_screening_pass_mark)
{
env.dbgPrintfTS("stopping reading fingerprints on bit %d/%d; have %d molecules to check... ",
_screening.query_bit_idx, _screening.query_ones.size(), _screening.passed.size());
_unmatched += _screening.block->used - _screening.passed.size();
break;
}
}
if (entire)
{
for (i = 0; i < _screening.block->used; i++)
{
if (_context.similarity.match(target_ones[i], _screening.one_counters[i]))
{
OraRowidText &rid = matched.at(matched.add());
storage.get(fingerprints.getStorageIndex_NoMap(_screening, i), stored);
_decompressRowid(stored, rid);
_matched++;
}
else
_unmatched++;
}
}
else if (_screening.passed.size() > 0)
{
profTimerStart(tfine, "sim.fetch.fine");
for (i = _screening.passed.begin(); i != _screening.passed.end(); i = _screening.passed.next(i))
_match(env, fingerprints.getStorageIndex_NoMap(_screening, _screening.passed[i]));
profTimerStop(tfine);
}
env.dbgPrintf("done\n");
fingerprints.countOnes_End(env, _screening);
}
profTimerStop(tsimfetch);
}
