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 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);
}
}