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()); }