void CVecscreenRun::x_RunBlast()
{
//_ASSERT(m_Queries.NotEmpty());
//_ASSERT(m_Queries->Size() != 0);
// Load blast queries
CRef<IQueryFactory> query_factory(new CObjMgr_QueryFactory(*m_Queries));
// BLAST optiosn needed for vecscreen.
CRef<CBlastOptionsHandle> opts(CBlastOptionsFactory::CreateTask("vecscreen"));
// Sets Vecscreen database.
const CSearchDatabase target_db(m_DB, CSearchDatabase::eBlastDbIsNucleotide);
// Constructor for blast run.
CLocalBlast blaster(query_factory, opts, target_db);
// BLAST run.
m_RawBlastResults = blaster.Run();
_ASSERT(m_RawBlastResults->size() == 1);
CRef<CBlastAncillaryData> ancillary_data((*m_RawBlastResults)[0].GetAncillaryData());
// The vecscreen stuff follows.
m_Vecscreen = new CVecscreen(*((*m_RawBlastResults)[0].GetSeqAlign()), GetLength(*m_SeqLoc, m_Scope));
// This actually does the vecscreen work.
m_Seqalign_set = m_Vecscreen->ProcessSeqAlign();
CConstRef<CSeq_id> id(m_SeqLoc->GetId());
CRef<CSearchResults> results(new CSearchResults(id, m_Seqalign_set,
TQueryMessages(),
ancillary_data));
m_RawBlastResults->clear();
m_RawBlastResults->push_back(results);
}
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;
}
