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 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 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
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
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 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 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 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 CBDBEnvKeeperApp::Init(void)
{
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"BDB Environment Keeper");
SetupArgDescriptions(arg_desc.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 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 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 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 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());
}
void CTestMultipartCgiApplication::Init()
{
CCgiApplication::Init();
SetRequestFlags(CCgiRequest::fCaseInsensitiveArgs);
unique_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"Test of multipart CGI response implementation");
arg_desc->AddDefaultKey("mode", "mode", "Multipart mode",
CArgDescriptions::eString, "none");
arg_desc->SetConstraint
("mode",
&(*new CArgAllow_Strings, "none", "mixed", "related", "replace"));
SetupArgDescriptions(arg_desc.release());
}
void CTitleTester::Init(void)
{
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"Show a sequence's title", false);
arg_desc->AddKey("gi", "SeqEntryID", "GI id of the Seq-Entry to examine",
CArgDescriptions::eInteger);
arg_desc->AddKey("in", "GIList", "File listing GIs to look up",
CArgDescriptions::eInputFile);
arg_desc->SetDependency("gi", CArgDescriptions::eExcludes, "in");
arg_desc->AddFlag("reconstruct", "Reconstruct title");
arg_desc->AddFlag("allproteins", "Name all proteins, not just the first");
arg_desc->AddFlag("localannots",
"Never use related sequences' annotations");
SetupArgDescriptions(arg_desc.release());
}
void CTestNetScheduleClient::Init(void)
{
InitOutputBuffer();
CONNECT_Init();
SetDiagPostFlag(eDPF_Trace);
SetDiagPostLevel(eDiag_Info);
// 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 client");
arg_desc->AddKey("service", "ServiceName",
"NetSchedule service name (format: host:port or servcie_name)",
CArgDescriptions::eString);
arg_desc->AddKey("queue", "QueueName",
"NetSchedule queue name",
CArgDescriptions::eString);
arg_desc->AddOptionalKey("ilen", "InputLength", "Average input length",
CArgDescriptions::eInteger);
arg_desc->AddOptionalKey("maxruntime", "MaxRunTime",
"Maximum run time of this test", CArgDescriptions::eInteger);
arg_desc->AddOptionalKey("input", "InputString", "Input string",
CArgDescriptions::eString);
arg_desc->AddOptionalKey("jobs", "jobs", "Number of jobs to submit",
CArgDescriptions::eInteger);
arg_desc->AddOptionalKey("naff", "AffinityTokens",
"Number of different affinities", CArgDescriptions::eInteger);
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
}
// ============================================================================
void CFormatGuessApp::Init(void)
// ============================================================================
{
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext
(GetArguments().GetProgramBasename(),
"CFormatGuess front end: Guess various file formats");
//
// shared flags and parameters:
//
arg_desc->AddDefaultKey
("i", "InputFile",
"Input File Name or '-' for stdin.",
CArgDescriptions::eInputFile,
"-");
arg_desc->AddFlag(
"canonical-name",
"Use the canonical name which is the name of the format as "
"given by the underlying C++ format guesser.");
arg_desc->AddFlag(
"show-object-type",
"Make output include the type of the object. If it cannot be "
"determined or does not make sense for the given format then it "
"considers it 'unknown'"
);
arg_desc->AddDefaultKey(
"output-format", "OutputFormat",
"How this program should send the results of its guesses.",
CArgDescriptions::eString,
"text"
);
arg_desc->SetConstraint("output-format", &(*new CArgAllow_Strings,
"text", "XML"));
SetupArgDescriptions(arg_desc.release());
}
void CTestApplication::Init(void)
{
// Set error posting and tracing on maximum
SetDiagTrace(eDT_Enable);
SetDiagPostFlag(eDPF_All);
SetDiagPostLevel(eDiag_Info);
// Create command-line argument descriptions class
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(), "Test inter-process locks");
// Specific to multi-process configuration test
arg_desc->AddDefaultKey("test", "number", "test case number (internal use only)",
CArgDescriptions::eInteger, "0");
arg_desc->AddDefaultKey("lock", "name", "parent's lock (internal use only)",
CArgDescriptions::eString, kEmptyStr);
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
}
void CTestCompartApplication::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->AddDefaultKey("i", "InputFile",
"File of ASN text Seq-aligns",
CArgDescriptions::eInputFile,
"-");
arg_desc->AddDefaultKey("o", "OutputFile",
"File of results",
CArgDescriptions::eOutputFile,
"-");
arg_desc->AddFlag("allow-intersect",
"Permit compartments to contain intersecting alignments "
"provided the alignments are consistent");
arg_desc->AddFlag("allow-intersect-query",
"Permit compartments to contain intersecting alignments "
"for the query only");
arg_desc->AddFlag("allow-intersect-subject",
"Permit compartments to contain intersecting alignments "
"for the subject only");
arg_desc->AddFlag("allow-intersect-both",
"Permit compartments to contain intersecting alignments "
"only if both query and subject intersect");
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
}
void CTestApplication::Init(void)
{
CONNECT_Init(&GetConfig());
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->AddDefaultKey("gi_from", "GiFrom",
"first GI to fetch",
CArgDescriptions::eInt8, "100");
arg_desc->AddDefaultKey("gi_to", "GiTo",
"last GI to fetch",
CArgDescriptions::eInt8, "200");
arg_desc->AddDefaultKey("count", "Count",
"number of passes",
CArgDescriptions::eInteger, "1");
// Program description
string prog_description = "Test id1 reader\n";
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
prog_description, false);
// Pass argument descriptions to the application
//
SetupArgDescriptions(arg_desc.release());
}
void CVecScreenApp::Init()
{
HideStdArgs(fHideLogfile | fHideConffile | fHideFullVersion | fHideXmlHelp | fHideDryRun);
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"Vector screening tool, version " +
CVecScreenVersion().Print());
arg_desc->SetCurrentGroup("Input query options");
arg_desc->AddDefaultKey(kArgQuery, "input_file",
"Input file name",
CArgDescriptions::eInputFile, kDfltArgQuery);
arg_desc->SetCurrentGroup("BLAST database options");
arg_desc->AddDefaultKey(kArgDb, "dbname", "BLAST database name",
CArgDescriptions::eString, kDefaultVectorDb);
arg_desc->SetCurrentGroup("Output configuration options");
arg_desc->AddDefaultKey(kArgOutput, "output_file", "Output file name",
CArgDescriptions::eOutputFile, "-");
//arg_desc->AddDefaultKey("outfmt", "format",
arg_desc->AddDefaultKey(kArgOutputFormat, "format",
"VecScreen results options:\n"
" 0 = Show alignments pairwise,\n"
" 1 = Do not show alignments, just contaminated range offsets\n",
CArgDescriptions::eInteger,
NStr::IntToString(kDfltArgOutputFormat));
arg_desc->SetConstraint(kArgOutputFormat,
new CArgAllowValuesBetween(0, CVecscreenRun::CFormatter::eEndValue-1, true));
// Produce Text output?
arg_desc->AddFlag("text_output", "Produce text output?", true);
arg_desc->SetCurrentGroup("");
SetupArgDescriptions(arg_desc.release());
}
void CSampleLds2Application::Init(void)
{
// Prepare command line descriptions
//
// Create
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
arg_desc->AddOptionalKey("data_dir", "DataDir",
"Directory with the data files.", CArgDescriptions::eString);
arg_desc->AddKey("db", "DbFile", "LDS2 database file name.",
CArgDescriptions::eString);
// GI to fetch
arg_desc->AddKey("id", "SeqEntryID", "ID of the Seq-Entry to fetch",
CArgDescriptions::eString);
arg_desc->AddFlag("print_entry", "Print seq-entry");
arg_desc->AddFlag("print_feats", "Print features");
arg_desc->AddFlag("print_aligns", "Print alignments");
arg_desc->AddOptionalKey("group_aligns", "group_size",
"Group standalone seq-aligns into blobs",
CArgDescriptions::eInteger);
// Program description
string prog_description = "Example of the LDS2 usage\n";
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
prog_description, false);
// Pass argument descriptions to the application
//
SetupArgDescriptions(arg_desc.release());
}
void CCompartApplication::Init(void)
{
// Create command-line argument descriptions class
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
"makes compartments from protein BLAST m8");
CCompartOptions::SetupArgDescriptions(arg_desc.get());
arg_desc->AddDefaultKey("ifmt", "InputFormat",
"Format for input",
CArgDescriptions::eString,
"");
arg_desc->SetConstraint("ifmt",
&(*new CArgAllow_Strings,
"tabular", "seq-align", "seq-align-set", "seq-annot"));
arg_desc->AddFlag("hits",
"print hits");
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
}
void CAlnMrgApp::Init(void)
{
// Create command-line argument descriptions class
auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
// Specify USAGE context
arg_desc->SetUsageContext
(GetArguments().GetProgramBasename(),
"Alignment merger demo program");
// Describe the expected command-line arguments
arg_desc->AddDefaultKey
("in", "input_file_name",
"Name of file to read from (standard input by default)",
CArgDescriptions::eInputFile, "-");
arg_desc->AddDefaultKey
("asnout", "asn_out_file_name",
"Text ASN output",
CArgDescriptions::eOutputFile, "-");
arg_desc->AddOptionalKey
("asnoutb", "asn_out_file_name_b",
"Text ASN output, to a file opened in binary mode (for MS-Win tests)",
CArgDescriptions::eOutputFile, CArgDescriptions::fBinary);
arg_desc->AddDefaultKey
("b", "bin_obj_type",
"This forced the input file to be read in binary ASN.1 mode\n"
"and specifies the type of the top-level ASN.1 object.\n",
CArgDescriptions::eString, "");
arg_desc->AddDefaultKey
("bout", "bool",
"This forced the output file to be written in binary ASN.1 mode.\n",
CArgDescriptions::eBoolean, "f");
arg_desc->AddOptionalKey
("log", "log_file_name",
"Name of log file to write to",
CArgDescriptions::eOutputFile, CArgDescriptions::fPreOpen);
arg_desc->AddDefaultKey
("dsout", "bool",
"Output in Dense-seg format",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("gapjoin", "bool",
"Consolidate segments of equal lens with a gap on the query sequence",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("mingap", "bool",
"Consolidate all segments with a gap on the query sequence",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("rmleadtrailgaps", "bool",
"Remove leading and trailing gaps",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("minusstrand", "bool",
"Minus strand on the refseq when merging.",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("fillunaln", "bool",
"Fill unaligned regions.",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("calcscore", "bool",
"Calculate each aligned seq pair score and use it when merging."
"(Don't stitch off ObjMgr for this).",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("sortseqsbyscore", "bool",
"Sort sequences by score.",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("sortinputbyscore", "bool",
"Sort input by score.",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("noobjmgr", "bool",
// ObjMgr is used to identify sequences and obtain a bioseqhandle.
// Also used to calc scores and determine the type of molecule
"Skip ObjMgr in identifying sequences, calculating scores, etc.",
CArgDescriptions::eBoolean, "f");
arg_desc->AddOptionalKey
("se_in", "SeqEntryInputFile",
"An optional Seq-entry file to load a local top level seq entry from.",
CArgDescriptions::eInputFile, CArgDescriptions::fPreOpen);
arg_desc->AddOptionalKey
("fasta_in", "FastaFile",
"An optional FASTA file to load into ObjMgr's scope.",
CArgDescriptions::eInputFile, CArgDescriptions::fPreOpen);
arg_desc->AddOptionalKey
("blastdb", "BlastDb",
"Add an optional BLAST dataloader to ObjMgr's scope.",
CArgDescriptions::eString);
arg_desc->AddDefaultKey
("queryseqmergeonly", "bool",
"Merge the query seq only, keep subject seqs on separate rows "
"(even if the same seq).",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("truncateoverlaps", "bool",
"Truncate overlaps",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("allowtranslocation", "bool",
"Allow translocation",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("forcetranslation", "bool",
"Force translation of nucleotides",
CArgDescriptions::eBoolean, "f");
arg_desc->AddDefaultKey
("preserverows", "bool",
"Preserve rows",
CArgDescriptions::eBoolean, "f");
// Viewing args:
arg_desc->AddOptionalKey
("v", "",
"View format:\n"
" 1. CSV table\n"
" 2. Print segments\n"
" 3. Print chunks\n"
" 4. Popset style using GetAlnSeqString\n"
" (memory efficient for large alns, but slower)\n"
" 5. Popset style using GetSeqString\n"
" (memory inefficient)\n"
" 6. Popset style using GetWholeAlnSeqString\n"
" (fastest, but memory inefficient)\n",
CArgDescriptions::eInteger);
arg_desc->AddOptionalKey
("a", "AnchorRow",
"Anchor row (zero based)",
CArgDescriptions::eInteger);
arg_desc->AddDefaultKey
("w", "ScreenWidth",
"Screen width for some of the viewers",
CArgDescriptions::eInteger, "60");
arg_desc->AddDefaultKey
("cf", "GetChunkFlags",
"Flags for GetChunks (CAlnMap::TGetChunkFlags)",
CArgDescriptions::eInteger, "0");
arg_desc->AddDefaultKey
("progress", "bool",
"Show progress feedback on stderr",
CArgDescriptions::eBoolean, "f");
// Setup arg.descriptions for this application
SetupArgDescriptions(arg_desc.release());
}
