bool CTestDiagApp::TestApp_Args(CArgDescriptions& args) { args.AddPositional("case_number", "case number", CArgDescriptions::eInteger); args.SetConstraint("case_number", new CArgAllow_Integers(1, 47)); return true; }
bool CTestCacheApp::TestApp_Args(CArgDescriptions& args) { args.AddDefaultKey("element_size", "ElementSize", "Size of a cache element", CArgDescriptions::eInt8, "100000"); args.AddDefaultKey("cache_size", "CacheSize", "Initial size of the cache", CArgDescriptions::eInt8, "200"); args.AddDefaultKey("size_type", "SizeType", "Cache size type", CArgDescriptions::eString, "ubyte"); args.SetConstraint("size_type", &(*new CArgAllow_Strings, "ubyte", "uint", "uint8", "byte")); return true; }
BEGIN_NCBI_SCOPE void CAVApp::Init(void) { // create command-line argument descriptions CArgDescriptions *argDescr = new CArgDescriptions(); // usage argDescr->SetUsageContext(GetArguments().GetProgramName(), "CDD Alignment Viewer"); // output type (required) argDescr->AddKey("type", "type", "one of: 'text' (unformatted), 'HTML', or 'FASTA'", argDescr->eString); argDescr->SetConstraint("type", (new CArgAllow_Strings())->Allow("text")->Allow("HTML")->Allow("FASTA")); // lowercase flag for FASTA argDescr->AddFlag("fasta_lc", "whether to show unaligned residues in lowercase in FASTA output"); // paragraph width (optional, default 60) argDescr->AddDefaultKey("width", "integer", "paragraph width", argDescr->eInteger, "60"); argDescr->SetConstraint("width", new CArgAllow_Integers(1, kMax_Int)); // conservation threshhold (optional, default 2.0) argDescr->AddDefaultKey("cons", "bits", "conservation threshhold (bit score)", argDescr->eDouble, "2.0"); argDescr->AddFlag("identity", "show identity, ignoring bit score"); // whether to output left/right tails argDescr->AddFlag("lefttails", "whether to show left tails"); argDescr->AddFlag("righttails", "whether to show right tails"); // whether to do condensed display argDescr->AddFlag("condensed", "condensed incompletely aligned columns (text/HTML only)"); // don't use colored backgrounds argDescr->AddFlag("no_color_bg", "don't use colored backgrounds for alignment paragraphs (HTML only)"); // ignore bad pairwise alignments argDescr->AddFlag("ignore_bad_aln", "ignore invalid pairwise alignments in input data"); // input file name (required) argDescr->AddPositional("in", "name of input file", argDescr->eString); SetupArgDescriptions(argDescr); }
///////////////////////////////////////////////////////////////////////////// // Init test bool CCSRATestApp::TestApp_Args(CArgDescriptions& args) { // Specify USAGE context args.SetUsageContext(GetArguments().GetProgramBasename(), "test_csra_loader_mt"); args.AddDefaultKey("accs", "Accessions", "comma separated SRA accession list", CArgDescriptions::eString, "SRR000010"); //"SRR000010,SRR389414,SRR494733,SRR505887,SRR035417"); args.AddOptionalKey("accs-file", "Accessions", "file with SRA accession list", CArgDescriptions::eInputFile); args.AddDefaultKey("iter-count", "IterationCount", "Number of read iterations", CArgDescriptions::eInteger, "10"); args.AddDefaultKey("iter-size", "IterationSize", "Number of sequential sequences in one iteration", CArgDescriptions::eInteger, "10"); args.AddFlag("verbose", "Print info about progress"); args.AddFlag("preload", "Try to preload libraries in main thread"); args.AddFlag("full-seq", "Load full sequence"); args.AddFlag("shared-scope", "Use shared scope in all threads"); args.AddFlag("reset-history", "Reset scope's history after each iteration"); args.AddFlag("reference-sequences", "Test reference sequences retrieval"); return true; }
void Cn3DNoWin::Init(void) { // turn off some Mesa-related env vars, irrelevant to off-screen rendering and not platform-indepdendent setenv("MESA_NO_3DNOW", "true", 1); setenv("MESA_NO_SSE", "true", 1); // setup the diagnostic stream SetDiagHandler(DisplayDiagnostic, NULL, NULL); SetDiagPostLevel(eDiag_Info); // report all messages SetDiagTrace(eDT_Default); // trace messages only when DIAG_TRACE env. var. is set UnsetDiagTraceFlag(eDPF_Location); #ifdef _DEBUG SetDiagPostFlag(eDPF_File); SetDiagPostFlag(eDPF_Line); #else UnsetDiagTraceFlag(eDPF_File); UnsetDiagTraceFlag(eDPF_Line); #endif // C++ object verification CSerialObject::SetVerifyDataGlobal(eSerialVerifyData_Always); CObjectIStream::SetVerifyDataGlobal(eSerialVerifyData_Always); CObjectOStream::SetVerifyDataGlobal(eSerialVerifyData_Always); // set up argument processing CArgDescriptions *argDescr = new CArgDescriptions(false); argDescr->SetUsageContext(GetArguments().GetProgramName(), "No-Window Cn3D"); // get data from file or network argDescr->AddOptionalKey("f", "file", "Ncbi-mime-asn1, Biostruc, or Cdd ASN.1 data file", argDescr->eString); argDescr->AddOptionalKey("d", "id", "MMDB or PDB ID", argDescr->eString); // model, for network or Biostruc load argDescr->AddOptionalKey("o", "model", "Model type to use for coordinates", argDescr->eString); argDescr->SetConstraint("o", (new CArgAllow_Strings)->Allow("alpha")->Allow("single")->Allow("PDB")); // controls for output argDescr->AddKey("p", "pngfile", "Output PNG file name", argDescr->eString); argDescr->AddKey("w", "width", "Output width in pixels", argDescr->eInteger); argDescr->AddKey("h", "height", "Output height in pixels", argDescr->eInteger); argDescr->AddFlag("i", "Create interlaced PNG"); // use favorite style argDescr->AddOptionalKey("s", "style", "Favorite style", argDescr->eString); SetupArgDescriptions(argDescr); }