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;
}
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);
}