void CGridCgiSampleApplication::x_SetupArgs()
{
// Disregard the case of CGI arguments
SetRequestFlags(CCgiRequest::fCaseInsensitiveArgs);
// Create CGI argument descriptions class
// (For CGI applications only keys can be used)
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"CGI sample application");
// Describe possible cmd-line and HTTP entries
// (optional)
arg_desc->AddOptionalKey("message",
"message",
"Message passed to CGI application",
CArgDescriptions::eString,
CArgDescriptions::fAllowMultiple);
arg_desc->AddOptionalKey("Cancel",
"Cancel",
"Cancel the job",
CArgDescriptions::eString);
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
}
void
CDbapiDriverSampleApp::Init()
{
// Create command-line argument descriptions class
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"DBAPI Sample Application");
// Describe the expected command-line arguments
arg_desc->AddDefaultKey("S", "server",
"Name of the SQL server to connect to",
CArgDescriptions::eString,
m_DefaultServerName);
arg_desc->AddDefaultKey("U", "username",
"User name",
CArgDescriptions::eString,
"DBAPI_test");
arg_desc->AddDefaultKey("P", "password",
"Password",
CArgDescriptions::eString,
"allowed");
arg_desc->AddDefaultKey("v", "version",
"TDS protocol version",
CArgDescriptions::eInteger,
NStr::IntToString(m_DefaultTDSVersion));
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
}
void
CDemoApp::Init()
{
// Create command-line argument descriptions class
unique_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"MySQL Sample Application");
// Describe the expected command-line arguments
arg_desc->AddKey("S", "server",
"Name of the SQL server to connect to",
CArgDescriptions::eString);
arg_desc->AddDefaultKey("U", "username",
"User name",
CArgDescriptions::eString,
"anyone");
arg_desc->AddDefaultKey("P", "password",
"Password",
CArgDescriptions::eString,
"allowed");
arg_desc->AddKey("D", "database",
"Name of a database",
CArgDescriptions::eString);
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
}
void CTestNSStorage::Init(void)
{
// Setup command line arguments and parameters
// Create command-line argument descriptions class
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"NetSchedule storage");
arg_desc->AddPositional("service",
"NetCache service name.", CArgDescriptions::eString);
arg_desc->AddOptionalKey("protocol",
"protocol",
"NetCache client protocl",
CArgDescriptions::eString);
arg_desc->SetConstraint("protocol",
&(*new CArgAllow_Strings(NStr::eNocase),
"simple", "persistent")
);
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
// CONNECT_Init(&GetConfig());
// SetDiagPostLevel(eDiag_Info);
// SetDiagTrace(eDT_Enable);
}
void CLocalFinderApp::Init(void)
{
// Prepare command line descriptions
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->AddKey("input", "FastaFile",
"File containing FASTA-format sequence",
CArgDescriptions::eInputFile);
arg_desc->AddDefaultKey("from", "From",
"From",
CArgDescriptions::eInteger,
"0");
arg_desc->AddDefaultKey("to", "To",
"To",
CArgDescriptions::eInteger,
"1000000000");
arg_desc->AddKey("model", "ModelData",
"Model Data",
CArgDescriptions::eInputFile);
arg_desc->AddOptionalKey("align", "Alignments",
"Alignments",
CArgDescriptions::eInputFile);
arg_desc->AddFlag("rep", "Repeats");
// Pass argument descriptions to the application
//
SetupArgDescriptions(arg_desc.release());
}
void CTest::Init(void)
{
const size_t kUsageWidth = 90;
SetDiagPostLevel(eDiag_Error);
// To see all output, uncomment next line:
//SetDiagPostLevel(eDiag_Trace);
DisableArgDescriptions(fDisableStdArgs);
// Create command-line arguments
unique_ptr<CCommandArgDescriptions> cmd(new
CCommandArgDescriptions(true, 0, CCommandArgDescriptions::eCommandMandatory |
CCommandArgDescriptions::eNoSortCommands));
cmd->SetUsageContext(GetArguments().GetProgramBasename(),
"Test compression library (CArchive class)");
// test
{{
unique_ptr<CArgDescriptions> arg(new CArgDescriptions(false));
arg->SetUsageContext(kEmptyStr, "Run standard internal test.", false, kUsageWidth);
arg->AddDefaultPositional("fmt", "Compression format to test", CArgDescriptions::eString, "all");
arg->SetConstraint("fmt", &(*new CArgAllow_Strings, "all", "zip"));
cmd->AddCommand("test", arg.release());
}}
SetupArgDescriptions(cmd.release());
// Set base directory for file tests
m_TestDir = CDir::GetCwd();
}
void CTest::Init(void)
{
SetDiagPostLevel(eDiag_Warning);
unique_ptr<CArgDescriptions> d(new CArgDescriptions);
d->SetUsageContext("test_dll", "DLL accessory class");
SetupArgDescriptions(d.release());
}
void COMSSAMerge::Init()
{
auto_ptr<CArgDescriptions> argDesc(new CArgDescriptions);
argDesc->AddDefaultKey("i", "infiles",
"file containing list of input files on separate lines",
CArgDescriptions::eString,
"");
argDesc->AddFlag("sw", "output search results without spectra");
argDesc->AddFlag("it", "input as text asn.1 formatted search results");
argDesc->AddFlag("ib", "input as binary asn.1 formatted search results");
argDesc->AddFlag("ix", "input as xml formatted search results");
argDesc->AddFlag("ibz2", "input as xml formatted search results compressed by bzip2");
argDesc->AddPositional("o", "output file name", CArgDescriptions::eString);
argDesc->AddFlag("ot", "output as text asn.1 formatted search results");
argDesc->AddFlag("ob", "output as binary asn.1 formatted search results");
argDesc->AddFlag("ox", "output as xml formatted search results");
argDesc->AddFlag("obz2", "output as xml formatted search results compressed by bzip2");
argDesc->AddExtra(0,10000, "input file names", CArgDescriptions::eString);
SetupArgDescriptions(argDesc.release());
// allow info posts to be seen
SetDiagPostLevel(eDiag_Info);
}
void CThreadedServerApp::Init(void)
{
CORE_SetLOG(LOG_cxx2c());
CORE_SetLOCK(MT_LOCK_cxx2c());
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"sample server using thread pools");
arg_desc->AddKey("port", "N", "TCP port number on which to listen",
CArgDescriptions::eInteger);
arg_desc->SetConstraint("port", new CArgAllow_Integers(0, 0xFFFF));
arg_desc->AddDefaultKey("threads", "N", "Number of initial threads",
CArgDescriptions::eInteger, "5");
arg_desc->AddDefaultKey("maxThreads", "N",
"Maximum number of simultaneous threads",
CArgDescriptions::eInteger, "10");
arg_desc->AddDefaultKey("queue", "N", "Maximum size of request queue",
CArgDescriptions::eInteger, "20");
{{
CArgAllow* constraint = new CArgAllow_Integers(1, 999);
arg_desc->SetConstraint("threads", constraint);
arg_desc->SetConstraint("maxThreads", constraint);
arg_desc->SetConstraint("queue", constraint);
}}
SetupArgDescriptions(arg_desc.release());
}
void CBDB_TestThreads::Init(void)
{
SetDiagTrace(eDT_Enable);
SetDiagPostLevel(eDiag_Warning);
SetDiagPostFlag(eDPF_File);
SetDiagPostFlag(eDPF_Line);
SetDiagPostFlag(eDPF_Trace);
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext("test_bdb_threads",
"test BDB library with threads");
arg_desc->AddOptionalKey("recs",
"recs",
"Number of records to load per thread",
CArgDescriptions::eInteger);
arg_desc->AddOptionalKey("threads",
"threads",
"Number of concurrent threads",
CArgDescriptions::eInteger);
SetupArgDescriptions(arg_desc.release());
}
// --------------------------------------------------------------------------
void CAsn2FastaApp::Init(void)
// --------------------------------------------------------------------------
{
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(
GetArguments().GetProgramBasename(),
"Convert an ASN.1 Seq-entry into a FASTA report",
false);
// input
{{
// name
arg_desc->AddOptionalKey("i", "InputFile",
"Input file name", CArgDescriptions::eInputFile);
// input file serial format (AsnText\AsnBinary\XML, default: AsnText)
arg_desc->AddOptionalKey("serial", "SerialFormat", "Input file format",
CArgDescriptions::eString);
arg_desc->SetConstraint("serial", &(*new CArgAllow_Strings,
"text", "binary", "XML"));
// id
arg_desc->AddOptionalKey("id", "ID",
"Specific ID to display", CArgDescriptions::eString);
// input type:
arg_desc->AddDefaultKey( "type", "AsnType", "ASN.1 object type",
CArgDescriptions::eString, "any" );
arg_desc->SetConstraint( "type",
&( *new CArgAllow_Strings, "any", "seq-entry", "bioseq", "bioseq-set" ) );
// filtering options:
arg_desc->AddFlag("nucs-only", "Only emit nucleotide sequences");
arg_desc->AddFlag("prots-only", "Only emit protein sequences");
}}
// batch processing
{{
arg_desc->AddFlag("batch", "Process NCBI release file");
// compression
arg_desc->AddFlag("c", "Compressed file");
// propogate top descriptors
arg_desc->AddFlag("p", "Propogate top descriptors");
arg_desc->AddFlag("defline-only",
"Only output the defline");
}}
// output
{{
arg_desc->AddFlag("show-mods", "Show FASTA header mods (e.g. [strain=abc])");
// name
arg_desc->AddOptionalKey("o", "OutputFile",
"Output file name", CArgDescriptions::eOutputFile);
}}
SetupArgDescriptions(arg_desc.release());
}
void CTestTransmission::Init(void)
{
SetDiagPostLevel(eDiag_Warning);
unique_ptr<CArgDescriptions> d(new CArgDescriptions);
d->SetUsageContext("test_transmissionrw",
"test transmission reader/writer");
SetupArgDescriptions(d.release());
}
void CDBAPI_CacheTest::Init(void)
{
SetDiagPostLevel(eDiag_Warning);
SetDiagPostFlag(eDPF_File);
SetDiagPostFlag(eDPF_Line);
auto_ptr<CArgDescriptions> d(new CArgDescriptions);
d->SetUsageContext("test_bdb", "test BDB library");
SetupArgDescriptions(d.release());
}
void CTestTable::Init(void)
{
SetDiagPostLevel(eDiag_Warning);
auto_ptr<CArgDescriptions> d(new CArgDescriptions);
d->SetUsageContext("test_table",
"test NCBI table");
SetupArgDescriptions(d.release());
}
void CBDBEnvKeeperApp::Init(void)
{
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"BDB Environment Keeper");
SetupArgDescriptions(arg_desc.release());
}
void CTestIdMux::Init(void)
{
SetDiagPostLevel(eDiag_Warning);
unique_ptr<CArgDescriptions> d(new CArgDescriptions);
d->SetUsageContext("test_id_mux",
"test id mux-demux");
SetupArgDescriptions(d.release());
}
void CBDB_PhoneBookDemo1::Init(void)
{
SetDiagPostLevel(eDiag_Warning);
SetDiagPostFlag(eDPF_File);
SetDiagPostFlag(eDPF_Line);
auto_ptr<CArgDescriptions> d(new CArgDescriptions);
d->SetUsageContext("bdb demo1",
"Demo1 application for BDB library");
SetupArgDescriptions(d.release());
}
//-------------------------------------------------------------------------
void CWinMaskApplication::Init(void)
{
HideStdArgs(fHideLogfile | fHideConffile | fHideVersion | fHideDryRun);
auto_ptr< CArgDescriptions > arg_desc( new CArgDescriptions );
// Set the program description
arg_desc->SetUsageContext( GetArguments().GetProgramBasename(),
USAGE_LINE );
CWinMaskConfig::AddWinMaskArgs(*arg_desc);
// Parse the arguments according to descriptions.
SetupArgDescriptions(arg_desc.release());
}
void CTestRangeMap::Init(void)
{
SetDiagPostLevel(eDiag_Warning);
auto_ptr<CArgDescriptions> d(new CArgDescriptions);
d->SetUsageContext("testrangemap",
"test different interval search classes");
d->AddDefaultKey("t", "type",
"type of container to use",
CArgDescriptions::eString, "CIntervalTree");
d->SetConstraint("t", (new CArgAllow_Strings)->
Allow("CIntervalTree")->Allow("i")->
Allow("CRangeMap")->Allow("r"));
d->AddDefaultKey("c", "count",
"how may times to run whole test",
CArgDescriptions::eInteger, "1");
d->AddFlag("s",
"silent operation - do not print log");
d->AddFlag("ps",
"print total number of intervals");
d->AddFlag("psn",
"print total number of scanned intervals");
d->AddDefaultKey("n", "rangeNumber",
"number of intervals to use",
CArgDescriptions::eInteger, "10000");
d->AddDefaultKey("l", "length",
"length of whole region",
CArgDescriptions::eInteger, "1000");
d->AddDefaultKey("il", "intervalLength",
"max length of intervals to use",
CArgDescriptions::eInteger, "20")
;
d->AddDefaultKey("ss", "scanStep",
"step of scan intervals",
CArgDescriptions::eInteger, "10");
d->AddDefaultKey("sl", "scanLength",
"length of scan intervals",
CArgDescriptions::eInteger, "20");
d->AddDefaultKey("sc", "scanCount",
"how may times to run scan test",
CArgDescriptions::eInteger, "1");
SetupArgDescriptions(d.release());
}
void CBlastDemoApplication::Init(void)
{
// Create command-line argument descriptions class
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(), "BLAST demo program");
arg_desc->AddKey
("program", "ProgramName",
"One of blastn, megablast, disc_megablast, blastp, blastx, tblastn, tblastx, rpsblast",
CArgDescriptions::eString);
arg_desc->SetConstraint
("program", &(*new CArgAllow_Strings,
"blastn", "megablast", "disc_megablast", "blastp", "blastx", "tblastn", "tblastx", "rpsblast"));
arg_desc->AddDefaultKey
("db", "DataBase",
"This is the name of the database",
CArgDescriptions::eString, "nr");
arg_desc->AddDefaultKey("in", "Queryfile",
"A FASTA file with the query", CArgDescriptions::eInputFile, "stdin");
arg_desc->AddDefaultKey("parse", "parse", "Parse FASTA defline",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey("out", "Outputfile",
"The output file", CArgDescriptions::eOutputFile, "stdout");
arg_desc->AddDefaultKey("evalue", "evalue",
"E-value threshold for saving hits", CArgDescriptions::eDouble, "0");
arg_desc->AddDefaultKey("penalty", "penalty", "Penalty score for a mismatch",
CArgDescriptions::eInteger, "0");
arg_desc->AddDefaultKey("reward", "reward", "Reward score for a match",
CArgDescriptions::eInteger, "0");
arg_desc->AddDefaultKey("matrix", "matrix", "Scoring matrix name",
CArgDescriptions::eString, "BLOSUM62");
arg_desc->AddDefaultKey("hitsize", "hitsize", "Hitlist size",
CArgDescriptions::eInteger, "100");
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
}
void CSeqDBPerfApp::Init()
{
HideStdArgs(fHideConffile | fHideFullVersion | fHideXmlHelp | fHideDryRun);
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"CSeqDB performance testing client");
arg_desc->SetCurrentGroup("BLAST database options");
arg_desc->AddDefaultKey("db", "dbname", "BLAST database name",
CArgDescriptions::eString, "nr");
arg_desc->AddDefaultKey("dbtype", "molecule_type",
"Molecule type stored in BLAST database",
CArgDescriptions::eString, "guess");
arg_desc->SetConstraint("dbtype", &(*new CArgAllow_Strings,
"nucl", "prot", "guess"));
arg_desc->SetCurrentGroup("Retrieval options");
arg_desc->AddFlag("scan_uncompressed",
"Do a full database scan of uncompressed sequence data", true);
arg_desc->AddFlag("scan_compressed",
"Do a full database scan of compressed sequence data", true);
arg_desc->AddFlag("get_metadata",
"Retrieve BLAST database metadata", true);
arg_desc->SetDependency("scan_compressed", CArgDescriptions::eExcludes,
"scan_uncompressed");
arg_desc->SetDependency("scan_compressed", CArgDescriptions::eExcludes,
"get_metadata");
arg_desc->SetDependency("scan_uncompressed", CArgDescriptions::eExcludes,
"get_metadata");
arg_desc->AddDefaultKey("num_threads", "number",
"Number of threads to use (requires OpenMP)",
CArgDescriptions::eInteger, "1");
arg_desc->SetConstraint("num_threads", new CArgAllow_Integers(0, kMax_Int));
//arg_desc->AddFlag("one_db_handle", "Build only 1 CSeqDB object?", true);
//arg_desc->SetDependency("one_db_handle", CArgDescriptions::eRequires, "num_threads");
arg_desc->SetCurrentGroup("Output configuration options");
arg_desc->AddDefaultKey("out", "output_file", "Output file name",
CArgDescriptions::eOutputFile, "-");
SetupArgDescriptions(arg_desc.release());
}
void CTest::Init(void)
{
SetDiagPostLevel(eDiag_Error);
// To see all output, uncomment next line:
//SetDiagPostLevel(eDiag_Trace);
// Create command-line argument descriptions
unique_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"Test compression library");
arg_desc->AddDefaultPositional
("lib", "Compression library to test", CArgDescriptions::eString, "all");
arg_desc->SetConstraint
("lib", &(*new CArgAllow_Strings, "all", "z", "bz2", "lzo"));
SetupArgDescriptions(arg_desc.release());
}
void CTestApplication::Init(void)
{
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"LDS test program");
arg_desc->AddOptionalKey("mklds", "mklds", "Index LDS directory",
CArgDescriptions::eString);
arg_desc->AddOptionalKey("ldsdir", "ldsdir", "Existing LDS directory to use",
CArgDescriptions::eString);
arg_desc->AddExtra(0, kMax_UInt, "IDs to check", CArgDescriptions::eString);
SetupArgDescriptions(arg_desc.release());
}
void CTest::Init(void)
{
unique_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"Test program for the C Logging API");
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
// Reset environment variables that can affect test output
putenv((char*)"SERVER_PORT=");
putenv((char*)"HTTP_NCBI_SID=");
putenv((char*)"HTTP_NCBI_PHID=");
putenv((char*)"NCBI_LOG_SESSION_ID=");
putenv((char*)"NCBI_LOG_HIT_ID=");
putenv((char*)"NCBI_CONFIG__LOG__FILE=");
}
void CImageTestApp::Init(void)
{
// Create command-line argument descriptions class
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"Image read/write test application");
arg_desc->AddDefaultKey("base", "ImageBase",
"Base of image name",
CArgDescriptions::eString, "test");
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
}
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);
}
void CTestApp::Init(void)
{
SetDiagPostLevel(eDiag_Warning);
SetDiagPostFlag(eDPF_All);
auto_ptr<CArgDescriptions> d(new CArgDescriptions);
d->SetUsageContext("test_strdbl",
"test string <-> double conversion");
d->AddFlag("speed",
"Run conversion speed benchmark");
d->AddOptionalKey("precision", "precision",
"Run conversion precision benchmark",
CArgDescriptions::eString);
d->SetConstraint("precision",
&(*new CArgAllow_Strings,
"Posix", "PosixOld", "strtod"));
d->AddDefaultKey("count", "count",
"Number of test iterations to run",
CArgDescriptions::eInteger, "1000000");
d->AddOptionalKey("test_strings", "test_strings",
"List of test strings to run",
CArgDescriptions::eString);
d->AddDefaultKey("verbose", "verbose",
"Verbose level",
CArgDescriptions::eInteger, "0");
d->AddDefaultKey("threshold", "threshold",
"Close match threshold",
CArgDescriptions::eDouble, "0.01");
d->AddFlag("randomize",
"Randomize test data (for precision and double-to-string tests)");
d->AddOptionalKey("seed", "Randomization",
"Randomization seed value",
CArgDescriptions::eInt8);
d->AddDefaultKey("digits", "significantDigits",
"The number of significant digits in double-to-string conversion",
CArgDescriptions::eInteger, NStr::NumericToString(DBL_DIG));
d->SetConstraint("digits", new CArgAllow_Integers(1, DBL_DIG));
d->AddDefaultKey("mode", "testmode",
"Test string-to-doube, or double-to-string",
CArgDescriptions::eString, "both");
d->SetConstraint( "mode", &(*new CArgAllow_Strings,
"str2dbl", "dbl2str", "both"));
SetupArgDescriptions(d.release());
}
void CTestDateApp::Init(void)
{
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"test of CDate_std::GetDate()");
arg_desc->AddKey("f", "format", "date format", CArgDescriptions::eString);
arg_desc->AddKey("Y", "year", "year number", CArgDescriptions::eInteger);
arg_desc->AddOptionalKey("M", "month", "month number",
CArgDescriptions::eInteger);
arg_desc->AddOptionalKey("D", "day", "day number",
CArgDescriptions::eInteger);
arg_desc->AddOptionalKey("S", "season", "season name",
CArgDescriptions::eString);
// hour, minute, second?
SetupArgDescriptions(arg_desc.release());
}
void CServerTestApp::Init(void)
{
CORE_SetLOCK(MT_LOCK_cxx2c());
CORE_SetLOG(LOG_cxx2c());
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"CServer test application");
arg_desc->AddDefaultKey("srvthreads", "N",
"Initial number of server threads",
CArgDescriptions::eInteger, "5");
arg_desc->AddDefaultKey("maxsrvthreads", "N",
"Maximum number of server threads",
CArgDescriptions::eInteger, "10");
arg_desc->AddDefaultKey("clthreads", "N",
"Initial number of client threads",
CArgDescriptions::eInteger, "5");
arg_desc->AddDefaultKey("maxclthreads", "N",
"Maximum number of client threads",
CArgDescriptions::eInteger, "10");
arg_desc->AddDefaultKey("requests", "N",
"Number of requests to make",
CArgDescriptions::eInteger, "100");
CArgAllow* constraint = new CArgAllow_Integers(1, 999);
arg_desc->SetConstraint("srvthreads", constraint);
arg_desc->SetConstraint("maxsrvthreads", constraint);
arg_desc->SetConstraint("clthreads", constraint);
arg_desc->SetConstraint("maxclthreads", constraint);
arg_desc->SetConstraint("requests", constraint);
arg_desc->AddDefaultKey("maxdelay", "N",
"Maximum delay in milliseconds",
CArgDescriptions::eInteger, "1000");
SetupArgDescriptions(arg_desc.release());
}
void CBamGraphTestApp::Init(void)
{
// Create command-line argument descriptions class
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"CArgDescriptions demo program");
arg_desc->AddOptionalKey("dir", "Dir",
"BAM files files directory",
CArgDescriptions::eString);
arg_desc->AddDefaultKey("file", "File",
"BAM file name",
CArgDescriptions::eString,
BAM_FILE);
arg_desc->AddOptionalKey("ref_label", "RefLabel",
"RefSeq id in BAM file",
CArgDescriptions::eString);
arg_desc->AddOptionalKey("seq_id", "SeqId",
"RefSeq Seq-id",
CArgDescriptions::eString);
arg_desc->AddFlag("log", "Generate logarithmic graph");
arg_desc->AddFlag("int", "Generate graph with int values");
arg_desc->AddOptionalKey("outlier_max", "OutlierMax",
"Factor over average to treat as outlier",
CArgDescriptions::eDouble);
arg_desc->AddOptionalKey("bin_size", "BinSize",
"Seq-graph bin size",
CArgDescriptions::eInteger);
arg_desc->AddOptionalKey("title", "Title",
"Title of generated Seq-graph",
CArgDescriptions::eString);
arg_desc->AddDefaultKey("o", "OutputFile",
"Output file of ASN.1",
CArgDescriptions::eOutputFile,
"-");
arg_desc->AddFlag("bin", "Write binary ASN.1");
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
}
