static int
process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_fmfile, char **ret_qfile)
{
ESL_GETOPTS *go = esl_getopts_Create(options);
int status;
if (esl_opt_ProcessEnvironment(go) != eslOK) { if (printf("Failed to process environment: %s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) { if (printf("Failed to parse command line: %s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if (esl_opt_VerifyConfig(go) != eslOK) { if (printf("Failed to parse command line: %s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
/* help format: */
if (esl_opt_GetBoolean(go, "-h") == TRUE)
{
esl_banner(stdout, argv[0], banner);
esl_usage(stdout, argv[0], usage);
if (puts("\nBasic options:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1= group; 2 = indentation; 120=textwidth*/
if (puts("\nSpecial options:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 2, 2, 80); /* 2= group; 2 = indentation; 120=textwidth*/
exit(0);
}
if (esl_opt_ArgNumber(go) != 2) { if (puts("Incorrect number of command line arguments.") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if ((*ret_qfile = esl_opt_GetArg(go, 1)) == NULL) { if (puts("Failed to get <qfile> argument on command line") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if ((*ret_fmfile = esl_opt_GetArg(go, 2)) == NULL) { if (puts("Failed to get <fmfile> argument on command line") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
/* Validate any attempted use of stdin streams */
if (esl_strcmp(*ret_fmfile, "-") == 0 && esl_strcmp(*ret_qfile, "-") == 0)
{ if (puts("Either <fmfile> or <qfile> may be '-' (to read from stdin), but not both.") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
*ret_go = go;
return eslOK;
FAILURE: /* all errors handled here are user errors, so be polite. */
esl_usage(stdout, argv[0], usage);
puts("\nwhere basic options are:");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1= group; 2 = indentation; 80=textwidth*/
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
esl_getopts_Destroy(go);
exit(1);
ERROR:
if (go) esl_getopts_Destroy(go);
exit(status);
}
static void
process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_hmmfile, char **ret_alifile)
{
ESL_GETOPTS *go = NULL;
if ((go = esl_getopts_Create(options)) == NULL) p7_Die("problem with options structure");
if (esl_opt_ProcessEnvironment(go) != eslOK) { printf("Failed to process environment: %s\n", go->errbuf); goto ERROR; }
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) { printf("Failed to parse command line: %s\n", go->errbuf); goto ERROR; }
if (esl_opt_VerifyConfig(go) != eslOK) { printf("Failed to parse command line: %s\n", go->errbuf); goto ERROR; }
/* help format: */
if (esl_opt_GetBoolean(go, "-h") == TRUE)
{
p7_banner(stdout, argv[0], banner);
esl_usage(stdout, argv[0], usage);
puts("\nwhere basic options are:");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
puts("\nOptions for selecting alphabet rather than guessing it:");
esl_opt_DisplayHelp(stdout, go, 2, 2, 80);
puts("\nAlternative model construction strategies:");
esl_opt_DisplayHelp(stdout, go, 3, 2, 80);
puts("\nAlternative relative sequence weighting strategies:");
esl_opt_DisplayHelp(stdout, go, 4, 2, 80);
puts("\nAlternate effective sequence weighting strategies:");
esl_opt_DisplayHelp(stdout, go, 5, 2, 80);
puts("\nControl of E-value calibration:");
esl_opt_DisplayHelp(stdout, go, 6, 2, 80);
puts("\nOther options:");
esl_opt_DisplayHelp(stdout, go, 8, 2, 80);
exit(0);
}
if (esl_opt_ArgNumber(go) != 2) { puts("Incorrect number of command line arguments."); goto ERROR; }
if ((*ret_hmmfile = esl_opt_GetArg(go, 1)) == NULL) { puts("Failed to get <hmmfile> argument on command line"); goto ERROR; }
if ((*ret_alifile = esl_opt_GetArg(go, 2)) == NULL) { puts("Failed to get <alifile> argument on command line"); goto ERROR; }
*ret_go = go;
return;
ERROR: /* all errors handled here are user errors, so be polite. */
esl_usage(stdout, argv[0], usage);
puts("\nwhere basic options are:");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
printf("\nTo see more help on other available options, do %s -h\n\n", argv[0]);
exit(1);
}
/* process_commandline()
*
* Processes the commandline, filling in fields in <cfg> and creating and returning
* an <ESL_GETOPTS> options structure. The help page (hmmsearch -h) is formatted
* here.
*/
static int
process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_hmmfile, char **ret_seqfile)
{
ESL_GETOPTS *go = esl_getopts_Create(options);
int status;
if (esl_opt_ProcessEnvironment(go) != eslOK) { if (printf("Failed to process environment: %s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) { if (printf("Failed to parse command line: %s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if (esl_opt_VerifyConfig(go) != eslOK) { if (printf("Failed to parse command line: %s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
/* help format: */
if (esl_opt_GetBoolean(go, "-h") == TRUE)
{
p7_banner(stdout, argv[0], banner);
esl_usage(stdout, argv[0], usage);
if (puts("\nBasic options:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1= group; 2 = indentation; 80=textwidth*/
if (puts("\nOptions controlling output:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 2, 2, 80);
if (puts("\nOptions controlling reporting thresholds:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 4, 2, 80);
if (puts("\nOptions controlling inclusion (significance) thresholds:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 5, 2, 80);
if (puts("\nOptions for model-specific thresholding:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 6, 2, 80);
if (puts("\nOptions controlling acceleration heuristics:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 7, 2, 80);
if (puts("\nOther expert options:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 12, 2, 80);
exit(0);
}
if (esl_opt_ArgNumber(go) != 2) { if (puts("Incorrect number of command line arguments.") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if ((*ret_hmmfile = esl_opt_GetArg(go, 1)) == NULL) { if (puts("Failed to get <hmmdb> argument on command line") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if ((*ret_seqfile = esl_opt_GetArg(go, 2)) == NULL) { if (puts("Failed to get <seqfile> argument on command line") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
/* Validate any attempted use of stdin streams */
if (strcmp(*ret_hmmfile, "-") == 0)
{ if (puts("nhmmscan cannot read <hmm database> from stdin stream, because it must have hmmpress'ed auxfiles") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
*ret_go = go;
return eslOK;
FAILURE: /* all errors handled here are user errors, so be polite. */
esl_usage(stdout, argv[0], usage);
if (puts("\nwhere most common options are:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1= group; 2 = indentation; 80=textwidth*/
if (printf("\nTo see more help on available options, do %s -h\n\n", argv[0]) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_getopts_Destroy(go);
exit(1);
ERROR:
if (go) esl_getopts_Destroy(go);
exit(status);
}
static int
process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_alifile, char **ret_postalifile)
{
ESL_GETOPTS *go = esl_getopts_Create(options);
int status;
if (esl_opt_ProcessEnvironment(go) != eslOK) { if (printf("Failed to process environment:\n%s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) { if (printf("Failed to parse command line:\n%s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if (esl_opt_VerifyConfig(go) != eslOK) { if (printf("Failed to parse command line:\n%s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
/* help format: */
if (esl_opt_GetBoolean(go, "-h") == TRUE)
{
p7_banner(stdout, argv[0], banner);
esl_usage(stdout, argv[0], usage);
if (puts("\nBasic options:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
if (puts("\nMask range options (format: --xxx 10-20,30-40 ) :") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 5, 2, 80);
if (puts("\nOptions for selecting alphabet rather than guessing it:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 2, 2, 80);
if (puts("\nAlternative model construction strategies:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 3, 2, 80);
if (puts("\nAlternative relative sequence weighting strategies:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 4, 2, 80);
if (puts("\nOther options:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
esl_opt_DisplayHelp(stdout, go, 8, 2, 80);
exit(0);
}
if (esl_opt_ArgNumber(go) > 2) { if (puts("Incorrect number of command line arguments.") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if ((*ret_alifile = esl_opt_GetArg(go, 1)) == NULL) { if (puts("Failed to get <msafile> argument on command line") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) {
if ((*ret_postalifile = esl_opt_GetArg(go, 2)) == NULL) { if (puts("Failed to get <postmsafile> argument on command line") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
}
if (strcmp(*ret_alifile, "-") == 0 && ! esl_opt_IsOn(go, "--informat"))
{ if (puts("Must specify --informat to read <alifile> from stdin ('-')") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
*ret_go = go;
return eslOK;
FAILURE: /* all errors handled here are user errors, so be polite. */
esl_usage(stdout, argv[0], usage);
puts("\nwhere basic options are:");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
printf("\nTo see more help on other available options, do:\n %s -h\n\n", argv[0]);
esl_getopts_Destroy(go);
exit(1);
ERROR:
if (go) esl_getopts_Destroy(go);
exit(status);
}
