void BingoPgSection::readSectionBitsCount(indigo::Array<int>& bits_number) {
bits_number.resize(_sectionInfo.n_structures);
bits_number.zerofill();
if(_bitsCountBuffers.size() == 0)
_bitsCountBuffers.resize(SECTION_BITSNUMBER_PAGES);
int data_len, str_idx;
unsigned short* buffer_data;
for (int buf_idx = 0; buf_idx < SECTION_BITSNUMBER_PAGES; ++buf_idx) {
if(buf_idx * SECTION_BITS_PER_BLOCK >= _sectionInfo.n_structures)
break;
BingoPgBuffer& bits_buffer = _bitsCountBuffers[buf_idx];
bits_buffer.readBuffer(_index, _offset + buf_idx + SECTION_META_PAGES, BINGO_PG_READ);
buffer_data = (unsigned short*) bits_buffer.getIndexData(data_len);
for (int page_str_idx = 0; page_str_idx < SECTION_BITS_PER_BLOCK; ++page_str_idx) {
str_idx = buf_idx * SECTION_BITS_PER_BLOCK + page_str_idx;
if (str_idx >= _sectionInfo.n_structures)
break;
bits_number[str_idx] = buffer_data[page_str_idx];
}
bits_buffer.changeAccess(BINGO_PG_NOLOCK);
}
}
unsigned short BingoPgBufferCacheBin::writeBin(indigo::Array<char>& bin_buf) {
/*
* If read strategy then it is an update so read the buffer in this function also
*/
if(bin_buf.sizeInBytes() > MAX_SIZE)
throw Error("internal error: can not add bin to the cache because is not enough space");
/*
* Prepare output offset
*/
unsigned short result = 0;
/*
* Prepare new array = size + buf
*/
indigo::Array<char> out_arr;
indigo::ArrayOutput ao(out_arr);
BingoPgCommon::DataProcessing::handleArray(bin_buf, 0, &ao);
/*
* Store data with it size
*/
_cache.copy(out_arr);
/*
* If read strategy then it is an update so write the buffer
*/
if(!_write) {
_writeCache();
}
return result;
}
void BingoPgIndex::readXyzItem(int section_idx, int mol_idx, indigo::Array<char>& xyz_buf) {
/*
* Prepare info for reading
*/
BingoPgSection& current_section = _jumpToSection(section_idx);
int map_block_idx = mol_idx / BINGO_MOLS_PER_MAPBLOCK;
int map_mol_idx = mol_idx % BINGO_MOLS_PER_MAPBLOCK;
BingoPgBufferCacheMap& map_cache = current_section.getMapBufferCache(map_block_idx);
elog(DEBUG1, "bingo: index: read xyz: start read structure %d for section = %d", mol_idx, section_idx);
/*
* Get xyz item
*/
ItemPointerData xyz_item;
map_cache.getXyzItem(map_mol_idx, xyz_item);
/*
* Check for correct block num
*/
dword block_num = ItemPointerGetBlockNumber(&xyz_item);
if(block_num == InvalidBlockNumber) {
xyz_buf.clear();
elog(DEBUG1, "bingo: index: read xyz: xyz is empty for structure %d for section = %d", mol_idx, section_idx);
return;
}
unsigned short block_offset = ItemPointerGetOffsetNumber(&xyz_item);
/*
* Read xyz buffer for a given offset
*/
BingoPgBufferCacheBin& bin_cache = current_section.getBinBufferCache(block_num);
bin_cache.readBin(block_offset, xyz_buf);
elog(DEBUG1, "bingo: index: read xyz: successfully read xyz of size %d for block %d offset %d", xyz_buf.size(), block_num, block_offset);
}
void BingoPgSection::_setBinData(indigo::Array<char>& buf, int& last_buf, ItemPointerData& item_data) {
if(buf.size() == 0) {
BINGO_PG_TRY {
ItemPointerSet(&item_data, InvalidBlockNumber, 0);
} BINGO_PG_HANDLE(throw Error("internal error: can not set block data: %s", message));
return;
}
void RingoPgSearchEngine::_prepareExactQueryStrings(indigo::Array<char>& what_clause_str, indigo::Array<char>& from_clause_str, indigo::Array<char>& where_clause_str) {
ArrayOutput what_clause(what_clause_str);
ArrayOutput from_clause(from_clause_str);
ArrayOutput where_clause(where_clause_str);
what_clause.printf("b_id");
from_clause.printf("%s", _shadowRelName.ptr());
dword ex_hash;
int bingo_res = ringoGetHash(0, &ex_hash);
CORE_HANDLE_ERROR(bingo_res, 1, "reaction search engine: error while getting hash", bingoGetError());
where_clause.printf("ex_hash=%d", ex_hash);
what_clause_str.push(0);
from_clause_str.push(0);
where_clause_str.push(0);
}
void MangoPgSearchEngine::_prepareExactTauStrings(indigo::Array<char>& what_clause_str, indigo::Array<char>& from_clause_str, indigo::Array<char>& where_clause_str) {
ArrayOutput what_clause(what_clause_str);
ArrayOutput from_clause(from_clause_str);
ArrayOutput where_clause(where_clause_str);
what_clause.printf("b_id");
from_clause.printf("%s", _shadowRelName.ptr());
const char* query_gross = mangoTauGetQueryGross();
if(query_gross == 0)
CORE_HANDLE_ERROR(0, 1, "molecule seach engine: error while constructing gross string", bingoGetError());
where_clause.printf("gross='%s' OR gross LIKE '%s H%%'", query_gross, query_gross);
what_clause_str.push(0);
from_clause_str.push(0);
where_clause_str.push(0);
}
void BingoPgIndex::readDictionary(indigo::Array<char>& dictionary) {
dictionary.clear();
if(_metaInfo.n_blocks_for_dictionary == 0)
return;
indigo::Array<char> buffer_dict;
int block_size = _metaInfo.n_blocks_for_dictionary + _metaInfo.offset_dictionary;
/*
* Read all buffers for dictionary
*/
for (int block_idx = _metaInfo.offset_dictionary; block_idx < block_size; ++block_idx) {
BingoPgBufferCacheBin buffer_cache(block_idx, _index, false);
/*
* Read and concat buffers
*/
buffer_cache.readBin(0, buffer_dict);
dictionary.concat(buffer_dict);
}
}
void MangoPgSearchEngine::_prepareExactQueryStrings(indigo::Array<char>& what_clause_str, indigo::Array<char>& from_clause_str, indigo::Array<char>& where_clause_str) {
int hash_elements_count, count, bingo_res;
dword hash;
ArrayOutput what_clause(what_clause_str);
ArrayOutput from_clause(from_clause_str);
ArrayOutput where_clause(where_clause_str);
what_clause.printf("sh.b_id");
bingo_res = mangoGetHash(false, -1, &hash_elements_count, &hash);
CORE_HANDLE_ERROR(bingo_res, 1, "molecule search engine: error while getting hash", bingoGetError());
if(hash_elements_count > MAX_HASH_ELEMENTS)
hash_elements_count = MAX_HASH_ELEMENTS;
from_clause.printf("%s sh", _shadowRelName.ptr());
for (int i = 0; i < hash_elements_count; i++)
from_clause.printf(", %s t%d", _shadowHashRelName.ptr(), i);
/*
* Create complex WHERE clause
*/
bool where_was_added = false;
if (hash_elements_count > 0) {
where_was_added = true;
/*
* molecule ids must be same
*/
where_clause.printf("sh.b_id = t0.b_id AND ");
for (int i = 1; i < hash_elements_count; i++)
where_clause.printf("t%d.b_id = t%d.b_id AND ", i - 1, i);
/*
* query components must match target components
*/
for (int i = 0; i < hash_elements_count; i++) {
bingo_res = mangoGetHash(false, i, &count, &hash);
CORE_HANDLE_ERROR(bingo_res, 1, "molecule search engine: error while getting hash", bingoGetError());
where_clause.printf("t%d.ex_hash = %d AND ", i, hash);
}
/*
* components count mast must target components count
*/
Array<char> rel;
bingo_res = mangoExactNeedComponentMatching();
CORE_HANDLE_ERROR(bingo_res, 0, "molecule search engine: error while getting need matching", bingoGetError());
if (bingo_res > 0)
rel.readString(">=", true);
else
rel.readString("=", true);
for (int i = 0; i < hash_elements_count; i++) {
if (i != 0)
where_clause.printf("AND ");
bingo_res = mangoGetHash(false, i, &count, &hash);
CORE_HANDLE_ERROR(bingo_res, 1, "molecule search engine: error while getting hash", bingoGetError());
where_clause.printf("t%d.f_count %s %d ", i, rel.ptr(), count);
}
}
bingo_res = mangoExactNeedComponentMatching();
CORE_HANDLE_ERROR(bingo_res, 0, "molecule search engine: error while getting need matching", bingoGetError());
if (bingo_res == 0) {
if (where_was_added)
where_clause.printf("AND ");
/*
* There must be no other components in target
*/
int query_fragments_count = 0;
for (int i = 0; i < hash_elements_count; i++) {
bingo_res = mangoGetHash(false, i, &count, &hash);
CORE_HANDLE_ERROR(bingo_res, 1, "molecule search engine: error while getting hash", bingoGetError());
query_fragments_count += count;
}
where_clause.printf("sh.fragments = %d", query_fragments_count);
}
what_clause_str.push(0);
from_clause_str.push(0);
where_clause_str.push(0);
}
