public IEnumerable <FetchedData> fetch(SqlConnection conn)
{
byte[] fp;
BingoCore.ringoGetQueryFingerprint(out fp);
// Search using fast index
_index_data.fingerprints.init(conn);
_index_data.storage.validate(conn);
IEnumerable <int> screened;
if (!_index_data.fingerprints.ableToScreen(fp))
{
screened = _index_data.storage.enumerateStorageIds(nextAfterStorageId);
}
else
{
screened = _index_data.fingerprints.screenSub(conn, fp, nextAfterStorageId);
}
int cache_index = 0;
foreach (int storage_id in screened)
{
if (_index_data.storage.isDeleted(storage_id, conn, ref cache_index))
{
continue;
}
byte[] data_with_cmf = _index_data.storage.get(storage_id, 4, -1, conn, ref cache_index);
int ret = BingoCore.lib.ringoMatchTargetBinary(data_with_cmf,
data_with_cmf.Length);
if (ret == -2)
{
throw new Exception(BingoCore.lib.bingoGetError());
}
if (ret == -1)
{
throw new Exception(BingoCore.lib.bingoGetWarning());
}
if (ret == 1)
{
int id = _index_data.storage.getInt(storage_id, 0, conn, ref cache_index);
FetchedData data = new FetchedData(id);
if (highlighting)
{
data.str = BingoCore.ringoGetHightlightedReaction();
}
yield return(data);
}
}
}
public IEnumerable<FetchedData> fetch (SqlConnection conn)
{
byte[] fp;
BingoCore.ringoGetQueryFingerprint(out fp);
// Search using fast index
_index_data.fingerprints.init(conn);
_index_data.storage.validate(conn);
IEnumerable<int> screened;
if (!_index_data.fingerprints.ableToScreen(fp))
screened = _index_data.storage.enumerateStorageIds(nextAfterStorageId);
else
screened = _index_data.fingerprints.screenSub(conn, fp, nextAfterStorageId);
int cache_index = 0;
foreach (int storage_id in screened)
{
if (_index_data.storage.isDeleted(storage_id, conn, ref cache_index))
continue;
byte[] data_with_cmf = _index_data.storage.get(storage_id, 4, -1, conn, ref cache_index);
int ret = BingoCore.lib.ringoMatchTargetBinary(data_with_cmf,
data_with_cmf.Length);
if (ret == -2)
throw new Exception(BingoCore.lib.bingoGetError());
if (ret == -1)
throw new Exception(BingoCore.lib.bingoGetWarning());
if (ret == 1)
{
int id = _index_data.storage.getInt(storage_id, 0, conn, ref cache_index);
FetchedData data = new FetchedData(id);
if (highlighting)
data.str = BingoCore.ringoGetHightlightedReaction();
yield return data;
}
}
}
public IEnumerable <FetchedData> fetch(SqlConnection conn)
{
ArrayList res_list = new ArrayList();
StringBuilder command_text = new StringBuilder();
command_text.Append("SELECT sh.id");
if (search_type == SearchType.EXACT)
{
command_text.Append(", sh.cmf");
if (need_xyz)
{
command_text.Append(", sh.xyz");
}
}
if (search_type == SearchType.GROSS)
{
command_text.Append(", gross");
}
if (search_type == SearchType.MASS)
{
command_text.Append(", mass");
}
command_text.AppendFormat(" FROM {0} sh", _index_data.shadowTable);
command_text.Append(table_copies);
StringBuilder final_where_clause = new StringBuilder();
if (where_clause.Length > 0)
{
final_where_clause.Append(" ( ");
final_where_clause.Append(where_clause);
final_where_clause.Append(" ) ");
}
if (nextAfterStorageId != null)
{
if (final_where_clause.Length > 0)
{
final_where_clause.Append(" and ");
}
final_where_clause.Append(" (");
final_where_clause.AppendFormat(" storage_id > {0} ", nextAfterStorageId.Value);
final_where_clause.Append(" )");
}
if (final_where_clause.Length > 0)
{
command_text.Append(" WHERE ");
command_text.Append(final_where_clause.ToString());
}
if (nextAfterStorageId.HasValue)
{
command_text.Append(" ORDER BY storage_id");
}
UTF8Encoding encoding = new UTF8Encoding();
using (SqlCommand cmd = new SqlCommand(command_text.ToString(), conn))
{
cmd.CommandTimeout = 3600;
using (SqlDataReader reader = cmd.ExecuteReader())
{
byte[] xyz = new byte[0];
while (reader.Read())
{
int id = Convert.ToInt32(reader[0]);
int res;
if (search_type == SearchType.EXACT)
{
byte[] cmf = (byte[])reader[1];
if (need_xyz)
{
xyz = (byte[])reader[2];
}
res = BingoCore.lib.mangoMatchTargetBinary(cmf, cmf.Length, xyz, xyz.Length);
}
else if (search_type == SearchType.GROSS)
{
byte[] gross = encoding.GetBytes((string)reader[1]);
res = BingoCore.lib.mangoMatchTarget(gross, gross.Length);
}
else if (search_type == SearchType.MASS)
{
res = 1;
}
else
{
throw new Exception("Search type is undefined");
}
if (res == -2)
{
throw new Exception(BingoCore.lib.bingoGetError());
}
if (res == -1)
{
throw new Exception(BingoCore.lib.bingoGetWarning());
}
if (res == 1)
{
FetchedData data = new FetchedData(id);
if (search_type == SearchType.MASS)
{
data.value = (float)reader[1];
}
yield return(data);
}
}
}
}
}
public IEnumerable<FetchedData> fetch (SqlConnection conn)
{
byte[] fp;
BingoCore.mangoGetQueryFingerprint(out fp);
// Search using fast index
_index_data.fingerprints.init(conn);
_index_data.storage.validate(conn);
int need_coords = BingoCore.lib.mangoNeedCoords();
byte[] xyz = new byte[0];
IEnumerable<int> screened;
if (search_type == SearchType.SUB)
{
if (!_index_data.fingerprints.ableToScreen(fp))
screened = _index_data.storage.enumerateStorageIds(nextAfterStorageId);
else
screened = _index_data.fingerprints.screenSub(conn, fp, nextAfterStorageId);
}
else
{
screened = _index_data.fingerprints.screenSim(conn, fp, nextAfterStorageId,
new BingoFingerprints.getBoundsDelegate(simGetMinMaxBounds));
}
int cache_index = 0;
foreach (int storage_id in screened)
{
if (_index_data.storage.isDeleted(storage_id, conn, ref cache_index))
continue;
// TODO: add match with xyz test for binary molecules
byte[] data_with_cmf = _index_data.storage.get(storage_id, 6, -1, conn, ref cache_index);
if (need_coords != 0)
{
xyz = _index_data.getXyz(storage_id, conn);
}
int ret = BingoCore.lib.mangoMatchTargetBinary(data_with_cmf,
data_with_cmf.Length, xyz, xyz.Length);
if (ret < 0)
{
// Exception has happend
// Extract id
int id = _index_data.storage.getInt(storage_id, 0, conn, ref cache_index);
string msg = "Undef";
if (ret == -2)
msg = BingoCore.lib.bingoGetError();
if (ret == -1)
msg = BingoCore.lib.bingoGetWarning();
throw new Exception(String.Format("Id = {0}: {1}", id, msg));
}
if (ret == 1)
{
// Extract id
int id = _index_data.storage.getInt(storage_id, 0, conn, ref cache_index);
FetchedData mol = new FetchedData(id);
if (highlighting)
{
if (need_coords == 0)
{
// Load xyz
byte[] xyz_found = _index_data.getXyz(storage_id, conn);
BingoCore.lib.mangoLoadTargetBinaryXyz(xyz_found, xyz_found.Length);
}
mol.str = BingoCore.mangoGetHightlightedMolecule();
}
if (search_type == SearchType.SIM)
BingoCore.lib.mangoSimilarityGetScore(out mol.value);
yield return mol;
}
}
}
public IEnumerable <FetchedData> fetch(SqlConnection conn)
{
byte[] fp;
BingoCore.mangoGetQueryFingerprint(out fp);
// Search using fast index
_index_data.fingerprints.init(conn);
_index_data.storage.validate(conn);
int need_coords = BingoCore.lib.mangoNeedCoords();
byte[] xyz = new byte[0];
IEnumerable <int> screened;
if (search_type == SearchType.SUB)
{
if (!_index_data.fingerprints.ableToScreen(fp))
{
screened = _index_data.storage.enumerateStorageIds(nextAfterStorageId);
}
else
{
screened = _index_data.fingerprints.screenSub(conn, fp, nextAfterStorageId);
}
}
else
{
screened = _index_data.fingerprints.screenSim(conn, fp, nextAfterStorageId,
new BingoFingerprints.getBoundsDelegate(simGetMinMaxBounds));
}
int cache_index = 0;
foreach (int storage_id in screened)
{
if (_index_data.storage.isDeleted(storage_id, conn, ref cache_index))
{
continue;
}
// TODO: add match with xyz test for binary molecules
byte[] data_with_cmf = _index_data.storage.get(storage_id, 6, -1, conn, ref cache_index);
if (need_coords != 0)
{
xyz = _index_data.getXyz(storage_id, conn);
}
int ret = BingoCore.lib.mangoMatchTargetBinary(data_with_cmf,
data_with_cmf.Length, xyz, xyz.Length);
if (ret < 0)
{
// Exception has happend
// Extract id
int id = _index_data.storage.getInt(storage_id, 0, conn, ref cache_index);
string msg = "Undef";
if (ret == -2)
{
msg = BingoCore.lib.bingoGetError();
}
if (ret == -1)
{
msg = BingoCore.lib.bingoGetWarning();
}
throw new Exception(String.Format("Id = {0}: {1}", id, msg));
}
if (ret == 1)
{
// Extract id
int id = _index_data.storage.getInt(storage_id, 0, conn, ref cache_index);
FetchedData mol = new FetchedData(id);
if (highlighting)
{
if (need_coords == 0)
{
// Load xyz
byte[] xyz_found = _index_data.getXyz(storage_id, conn);
BingoCore.lib.mangoLoadTargetBinaryXyz(xyz_found, xyz_found.Length);
}
mol.str = BingoCore.mangoGetHightlightedMolecule();
}
if (search_type == SearchType.SIM)
{
BingoCore.lib.mangoSimilarityGetScore(out mol.value);
}
yield return(mol);
}
}
}
public IEnumerable<FetchedData> fetch (SqlConnection conn)
{
ArrayList res_list = new ArrayList();
StringBuilder command_text = new StringBuilder();
command_text.Append("SELECT sh.id");
if (search_type == SearchType.EXACT)
{
command_text.Append(", sh.cmf");
if (need_xyz)
command_text.Append(", sh.xyz");
}
if (search_type == SearchType.GROSS)
command_text.Append(", gross");
if (search_type == SearchType.MASS)
command_text.Append(", mass");
command_text.AppendFormat(" FROM {0} sh", _index_data.shadowTable);
command_text.Append(table_copies);
StringBuilder final_where_clause = new StringBuilder();
if (where_clause.Length > 0)
{
final_where_clause.Append(" ( ");
final_where_clause.Append(where_clause);
final_where_clause.Append(" ) ");
}
if (nextAfterStorageId != null)
{
if (final_where_clause.Length > 0)
final_where_clause.Append(" and ");
final_where_clause.Append(" (");
final_where_clause.AppendFormat(" storage_id > {0} ", nextAfterStorageId.Value);
final_where_clause.Append(" )");
}
if (final_where_clause.Length > 0)
{
command_text.Append(" WHERE ");
command_text.Append(final_where_clause.ToString());
}
if (nextAfterStorageId.HasValue)
command_text.Append(" ORDER BY storage_id");
UTF8Encoding encoding = new UTF8Encoding();
using (SqlCommand cmd = new SqlCommand(command_text.ToString(), conn))
{
cmd.CommandTimeout = 3600;
using (SqlDataReader reader = cmd.ExecuteReader())
{
byte[] xyz = new byte[0];
while (reader.Read())
{
int id = Convert.ToInt32(reader[0]);
int res;
if (search_type == SearchType.EXACT)
{
byte[] cmf = (byte[])reader[1];
if (need_xyz)
xyz = (byte[])reader[2];
res = BingoCore.lib.mangoMatchTargetBinary(cmf, cmf.Length, xyz, xyz.Length);
}
else if (search_type == SearchType.GROSS)
{
byte[] gross = encoding.GetBytes((string)reader[1]);
res = BingoCore.lib.mangoMatchTarget(gross, gross.Length);
}
else if (search_type == SearchType.MASS)
res = 1;
else
throw new Exception("Search type is undefined");
if (res == -2)
throw new Exception(BingoCore.lib.bingoGetError());
if (res == -1)
throw new Exception(BingoCore.lib.bingoGetWarning());
if (res == 1)
{
FetchedData data = new FetchedData(id);
if (search_type == SearchType.MASS)
data.value = (float)reader[1];
yield return data;
}
}
}
}
}
