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 heapblaster(int count, int locking) {
info_t info[THREADS] = {};
if (count < 1)
count = 1;
if (count >= THREADS)
count = THREADS;
printf("heapblaster: starting %d threads... (%s)\n",
count, locking ? "locking" : "not locking");
for (int n = 0; n < count; n++) {
info[n].lock = locking;
info[n].n = n;
if (count == 1) {
blaster(info + n);
return 0;
} else {
pthread_create(&info[n].t, NULL, blaster, info + n);
}
}
for (;;)
sleep(1000);
return 0;
}
void SeqSwapper::findBestPairings(const vector<int>& normal, const vector<int>& pending, vector< pair<int, int> >& pairs)
{
if ((normal.size() == 0) || (pending.size() == 0))
{
return;
}
//blast normal against pending
CdBlaster blaster(m_ac);
blaster.setQueryRows(&normal);
blaster.setSubjectRows(&pending);
blaster.setScoreType(CSeq_align::eScore_PercentIdentity);
blaster.blast();
//for each normal, find the hightest-scoring (in identity), unused and above the threshold pending
set<int> usedPendingIndice;
for (int n = 0; n < normal.size(); n++)
{
int maxId = 0;
int maxIdIndex = -1;
for (int p = 0; p < pending.size(); p++)
{
if (usedPendingIndice.find(p) == usedPendingIndice.end())//this pending has not been used
{
int pid = (int)blaster.getPairwiseScore(n, p);
if ((pid > maxId) && (pid >= m_replacingThreshold))
{
maxId = pid;
maxIdIndex = p;
}
}
}
if ( maxIdIndex >= 0)
{
usedPendingIndice.insert(maxIdIndex);
pairs.push_back(pair<int, int>(normal[n], pending[maxIdIndex]));
}
}
}
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;
}
