void test_query_batch() {
string error_msg;
vector<JOB_STATE> jobs;
int batch_id = 207;
const char* batch_name = "";
int retval = query_batch(
project_url, authenticator, batch_id, batch_name, jobs, error_msg
);
if (retval) {
printf("Error: %d (%s)\n", retval, error_msg.c_str());
return;
}
for (unsigned int i=0; i<jobs.size(); i++) {
JOB_STATE& js = jobs[i];
js.print();
}
}
int CVecScreenApp::Run(void)
{
int status = BLAST_EXIT_SUCCESS;
try {
// Allow the fasta reader to complain on invalid sequence input
SetDiagPostLevel(eDiag_Warning);
const bool kIsProtein(false);
/*** Process the command line arguments ***/
const CArgs& args = GetArgs();
const string kDbName(args[kArgDb].AsString());
CRef<CBlastOptionsHandle> opts_hndl(CBlastOptionsFactory::Create(eVecScreen));
/*** Initialize the scope ***/
SDataLoaderConfig dlconfig(kDbName, kIsProtein);
dlconfig.OptimizeForWholeLargeSequenceRetrieval();
CBlastInputSourceConfig iconfig(dlconfig);
iconfig.SetQueryLocalIdMode();
CRef<CScope> scope = CBlastScopeSource(dlconfig).NewScope();
/*** Initialize the input stream ***/
CBlastFastaInputSource fasta(args[kArgQuery].AsInputFile(), iconfig);
CBlastInput input(&fasta, 1);
/*** Get the formatting options ***/
const CVecscreenRun::CFormatter::TOutputFormat kFmt =
args[kArgOutputFormat].AsInteger();
const bool kHtmlOutput = !args["text_output"].AsBoolean();
/*** Process the input ***/
while ( !input.End() ) {
CRef<CBlastQueryVector> query_batch(input.GetNextSeqBatch(*scope));
_ASSERT(query_batch->Size() == 1);
CRef<IQueryFactory> queries(new CObjMgr_QueryFactory(*query_batch));
CVecscreenRun vs(CRef<CSeq_loc>(const_cast<CSeq_loc*>(&*query_batch->GetQuerySeqLoc(0))),
query_batch->GetScope(0), kDbName);
CVecscreenRun::CFormatter vs_format(vs, *scope, kFmt, kHtmlOutput);
vs_format.FormatResults(args[kArgOutput].AsOutputFile(), opts_hndl);
}
} CATCH_ALL(status)
return status;
}
