Exemplos de dlconfig em C++ (Cpp)

Exemplo n.º 1

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;
}

Exemplo n.º 2

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;
}