void CONFIG_Init(const CmdLineArgs& args)
{
TIMER(L"CONFIG_Init");
new CConfigDB;
// Load the global, default config file
g_ConfigDB.SetConfigFile(CFG_DEFAULT, L"config/default.cfg");
g_ConfigDB.Reload(CFG_DEFAULT); // 216ms
// Try loading the local system config file (which doesn't exist by
// default) - this is designed as a way of letting developers edit the
// system config without accidentally committing their changes back to SVN.
g_ConfigDB.SetConfigFile(CFG_SYSTEM, L"config/local.cfg");
g_ConfigDB.Reload(CFG_SYSTEM);
g_ConfigDB.SetConfigFile(CFG_USER, L"config/user.cfg");
g_ConfigDB.Reload(CFG_USER);
g_ConfigDB.SetConfigFile(CFG_MOD, L"config/mod.cfg");
// No point in reloading mod.cfg here - we haven't mounted mods yet
ProcessCommandLineArgs(args);
// Initialise console history file
int max_history_lines = 200;
CFG_GET_VAL("console.history.size", Int, max_history_lines);
g_Console->UseHistoryFile(L"config/console.txt", max_history_lines);
// Collect information from system.cfg, the profile file,
// and any command-line overrides to fill in the globals.
LoadGlobals(); // 64ms
}
int CBlastDemoApplication::Run(void)
{
// Get arguments
const CArgs& args = GetArgs();
EProgram program = ProgramNameToEnum(args["program"].AsString());
bool db_is_aa = (program == eBlastp || program == eBlastx ||
program == eRPSBlast || program == eRPSTblastn);
CRef<CBlastOptionsHandle> opts(CBlastOptionsFactory::Create(program, CBlastOptions::eRemote));
ProcessCommandLineArgs(opts);
opts->Validate(); // Can throw CBlastException::eInvalidOptions for invalid option.
// This will dump the options to stderr.
// opts->GetOptions().DebugDumpText(cerr, "opts", 1);
CRef<CObjectManager> objmgr = CObjectManager::GetInstance();
if (!objmgr) {
throw std::runtime_error("Could not initialize object manager");
}
const bool is_protein =
!!Blast_QueryIsProtein(opts->GetOptions().GetProgramType());
SDataLoaderConfig dlconfig(is_protein);
CBlastInputSourceConfig iconfig(dlconfig, objects::eNa_strand_other, false,
args["parse"].AsBoolean());
CBlastFastaInputSource fasta_input(args["in"].AsInputFile(), iconfig);
CScope scope(*objmgr);
CBlastInput blast_input(&fasta_input);
TSeqLocVector query_loc = blast_input.GetAllSeqLocs(scope);
CRef<IQueryFactory> query_factory(new CObjMgr_QueryFactory(query_loc));
const CSearchDatabase target_db(args["db"].AsString(),
db_is_aa ? CSearchDatabase::eBlastDbIsProtein : CSearchDatabase::eBlastDbIsNucleotide);
CRemoteBlast blaster(query_factory, opts, target_db);
// This will dump a lot of stuff to stderr.
// blaster.SetVerbose();
bool status = blaster.SubmitSync();
if (status == false)
throw std::runtime_error("No results returned by SubmitSync");
cerr << "RID: " << blaster.GetRID() << '\n';
CSearchResultSet results = *blaster.GetResultSet();
CNcbiOstream& out = args["out"].AsOutputFile();
for (unsigned int i = 0; i < results.GetNumResults(); i++) {
CConstRef<CSeq_align_set> sas = results[i].GetSeqAlign();
out << MSerial_AsnText << *sas;
}
return 0;
}