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; }