CRpsMmappedFile::CRpsMmappedFile(const string& filename)
{
try { m_MmappedFile.reset(new CMemoryFile(filename)); }
catch (const CFileException& e) {
NCBI_RETHROW(e, CBlastException, eRpsInit,
"Cannot memory map RPS-BLAST database file: " + filename);
}
}
void CId2Reader::x_ConnectAtSlot(TConn conn)
{
if ( GetDebugLevel() >= eTraceOpen ) {
CDebugPrinter s(conn, "CId2Reader");
s << "New connection to " << m_Connector.GetServiceName() << "...";
}
CReaderServiceConnector::SConnInfo conn_info = m_Connector.Connect();
CConn_IOStream& stream = *conn_info.m_Stream;
SetRandomFail(stream, conn);
if ( stream.bad() ) {
NCBI_THROW(CLoaderException, eConnectionFailed,
"cannot open connection: "+x_ConnDescription(stream));
}
if ( GetDebugLevel() >= eTraceOpen ) {
CDebugPrinter s(conn, "CId2Reader");
s << "New connection: " << x_ConnDescription(stream);
}
try {
x_InitConnection(stream, conn);
}
catch ( CException& exc ) {
m_Connector.RememberIfBad(conn_info);
NCBI_RETHROW(exc, CLoaderException, eConnectionFailed,
"connection initialization failed: "+
x_ConnDescription(stream));
}
SetRandomFail(stream, conn);
if ( stream.bad() ) {
NCBI_THROW(CLoaderException, eConnectionFailed,
"connection initialization failed: "+
x_ConnDescription(stream));
}
// successfully received reply, server is good, forget it
conn_info.MarkAsGood();
STimeout tmout;
m_Connector.SetTimeoutTo(&tmout);
CONN_SetTimeout(stream.GetCONN(), eIO_ReadWrite, &tmout);
tmout.sec = 0; tmout.usec = 1; // no wait on close
CONN_SetTimeout(stream.GetCONN(), eIO_Close, &tmout);
m_Connections[conn] = conn_info;
}
void CBlastRPSInfo::x_Init(const string& rps_dbname, int flags)
{
m_RpsInfo = NULL;
// Obtain the full path to the database
string path;
try {
vector<string> dbpath;
CSeqDB::FindVolumePaths(rps_dbname, CSeqDB::eProtein, dbpath);
path = *dbpath.begin();
} catch (const CSeqDBException& e) {
NCBI_RETHROW(e, CBlastException, eRpsInit,
"Cannot retrieve path to RPS database");
}
_ASSERT(!path.empty());
auto_ptr<BlastRPSInfo> rps_info;
// Allocate the core data structure
try { rps_info.reset(new BlastRPSInfo); }
catch (const bad_alloc&) {
NCBI_THROW(CBlastSystemException, eOutOfMemory,
"RPSInfo allocation failed");
}
// Assign the pointers to the core data structure
m_RpsInfo = rps_info.release();
m_RpsInfo->lookup_header = NULL;
m_RpsInfo->profile_header = NULL;
m_RpsInfo->freq_header = NULL;
m_RpsInfo->obsr_header = NULL;
m_RpsInfo->freq_ratios_header = NULL;
// Load the various files
if (flags & fAuxInfoFile) {
m_AuxFile.Reset(new CRpsAuxFile(path));
// Note that these const_casts are only needed because the data structure
// doesn't take const pointers, but these won't be modified at all
m_RpsInfo->aux_info =
*const_cast<BlastRPSAuxInfo*>((*m_AuxFile)());
}
if (flags & fLookupTableFile) {
m_LutFile.Reset(new CRpsLookupTblFile(path));
// Note that these const_casts are only needed because the data structure
// doesn't take const pointers, but these won't be modified at all
m_RpsInfo->lookup_header =
const_cast<BlastRPSLookupFileHeader*>((*m_LutFile)());
}
if (flags & fPssmFile) {
m_PssmFile.Reset(new CRpsPssmFile(path));
// Note that these const_casts are only needed because the data structure
// doesn't take const pointers, but these won't be modified at all
m_RpsInfo->profile_header =
const_cast<BlastRPSProfileHeader*>((*m_PssmFile)());
}
if (flags & fFrequenciesFile) {
m_FreqsFile.Reset(new CRpsFreqsFile(path));
// Note that these const_casts are only needed because the data structure
// doesn't take const pointers, but these won't be modified at all
m_RpsInfo->freq_header =
const_cast<BlastRPSProfileHeader*>((*m_FreqsFile)());
}
if (flags & fObservationsFile) {
m_ObsrFile.Reset(new CRpsObsrFile(path));
// Note that these const_casts are only needed because the data structure
// doesn't take const pointers, but these won't be modified at all
m_RpsInfo->obsr_header =
const_cast<BlastRPSProfileHeader*>((*m_ObsrFile)());
}
if (flags & fFreqRatiosFile) {
try {
// read frequency ratios data
m_FreqRatiosFile.Reset(new CRpsFreqRatiosFile(path));
} catch (const CBlastException& e) {
string msg = rps_dbname + " contains no frequency ratios needed for composition-based statistics.\n" \
"Please disable composition-based statistics when searching against " + rps_dbname + ".";
NCBI_RETHROW(e, CBlastException, eRpsInit, msg);
}
m_RpsInfo->freq_ratios_header =
const_cast<BlastRPSFreqRatiosHeader*>((*m_FreqRatiosFile)());
}
}
void CId2Reader::x_InitConnection(CConn_IOStream& stream, TConn conn)
{
// prepare init request
CID2_Request req;
req.SetRequest().SetInit();
x_SetContextData(req);
CID2_Request_Packet packet;
packet.Set().push_back(Ref(&req));
// that's it for now
// TODO: add params
// send init request
{{
if ( GetDebugLevel() >= eTraceConn ) {
CDebugPrinter s(conn, "CId2Reader");
s << "Sending";
if ( GetDebugLevel() >= eTraceASN ) {
s << ": " << MSerial_AsnText << packet;
}
else {
s << " ID2-Request-Packet";
}
s << "...";
}
try {
stream << MConnFormat << packet << flush;
}
catch ( CException& exc ) {
NCBI_RETHROW(exc, CLoaderException, eConnectionFailed,
"failed to send init request: "+
x_ConnDescription(stream));
}
if ( GetDebugLevel() >= eTraceConn ) {
CDebugPrinter s(conn, "CId2Reader");
s << "Sent ID2-Request-Packet.";
}
if ( !stream ) {
NCBI_THROW(CLoaderException, eConnectionFailed,
"failed to send init request: "+
x_ConnDescription(stream));
}
}}
// receive init reply
CID2_Reply reply;
{{
if ( GetDebugLevel() >= eTraceConn ) {
CDebugPrinter s(conn, "CId2Reader");
s << "Receiving ID2-Reply...";
}
stream >> MConnFormat >> reply;
if ( GetDebugLevel() >= eTraceConn ) {
CDebugPrinter s(conn, "CId2Reader");
s << "Received";
if ( GetDebugLevel() >= eTraceASN ) {
s << ": " << MSerial_AsnText << reply;
}
else {
s << " ID2-Reply.";
}
}
if ( !stream ) {
NCBI_THROW(CLoaderException, eLoaderFailed,
"failed to receive init reply: "+
x_ConnDescription(stream));
}
}}
// check init reply
if ( reply.IsSetDiscard() ) {
NCBI_THROW(CLoaderException, eLoaderFailed,
"bad init reply: 'discard' is set: "+
x_ConnDescription(stream));
}
if ( reply.IsSetError() ) {
NCBI_THROW(CLoaderException, eLoaderFailed,
"bad init reply: 'error' is set: "+
x_ConnDescription(stream));
}
if ( !reply.IsSetEnd_of_reply() ) {
NCBI_THROW(CLoaderException, eLoaderFailed,
"bad init reply: 'end-of-reply' is not set: "+
x_ConnDescription(stream));
}
if ( reply.GetReply().Which() != CID2_Reply::TReply::e_Init ) {
NCBI_THROW(CLoaderException, eLoaderFailed,
"bad init reply: 'reply' is not 'init': "+
x_ConnDescription(stream));
}
// that's it for now
// TODO: process params
}
