/////////////////////////////////////////////////////////////////////////////
// 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;
}
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);
}