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