bool TestExtOptions::test_getopt() {
f_getopt("");
return Count(true);
}
/* initenv () initializes the environment */
void initenv (int argc, char **argv, struct mngmsg *m_msp,
struct pstruct *ppst, unsigned char **aa0)
{
char *cptr, ctmp;
long l_tmp;
int copt, itmp, i;
/* options for all search functions */
/* char *g_optstr = "b:BC:d:DE:F:HiK:l:Lm:N:O:QqR:T:v:V:w:W:X:Z:"; */
char g_optstring[MAX_STR];
char f_optstring[MAX_STR];
char optstring[MAX_STR];
build_optstr(g_optstring, sizeof(f_optstring), g_options);
build_optstr(f_optstring, sizeof(f_optstring), f_options);
/* these initializations will be used by all functions */
/* prog_name[] is only used for error messages */
strncpy(prog_name,argv[0],sizeof(prog_name));
prog_name[sizeof(prog_name)-1]='\0';
#ifdef PCOMPLIB
#ifdef MPI_SRC
MPI_Comm_size(MPI_COMM_WORLD,&fa_max_workers);
if (fa_max_workers <= 1) {
fprintf(stderr," nnodes = %d; no workers available\n",fa_max_workers);
exit(1);
}
else {
fa_max_workers -= FIRSTNODE;
fprintf(stderr," have %d workers\n",fa_max_workers);
}
#endif
#else
#if defined(IRIX)
fa_max_workers = sysmp(MP_NPROCS);
#else
#if defined(UNIX) || defined(HAVE_SYSCONF)
fa_max_workers = sysconf(_SC_NPROCESSORS_CONF);
#endif /* UNIX || SYSCONF */
#endif /* !IRIX */
#endif /* !PCOMPLIB */
m_msp->ltitle[0] = '\0';
if ((cptr=getenv("FASTLIBS"))!=NULL) {
strncpy(m_msp->flstr,cptr,MAX_FN);
m_msp->flstr[MAX_FN-1] = '\0';
}
else m_msp->flstr[0]='\0';
m_msp->std_output = 1;
m_msp->hist.hist_a = NULL;
m_msp->outfile[0] = '\0';
m_msp->outfd = NULL;
m_msp->ldb_info.ldnaseq = SEQT_PROT; /* library is protein */
m_msp->n1_low = ppst->n1_low = 0;
m_msp->n1_high = ppst->n1_high = BIGNUM;
m_msp->ql_start = 1; /* start with first query sequence */
m_msp->ql_stop = BIGNUM; /* end with the last query sequence */
m_msp->aa1save_buf_b = NULL;
m_msp->bline_buf_b = NULL;
m_msp->pamd1 = MAXSQ;
m_msp->pamd2 = MAXSQ;
m_msp->ldb_info.term_code = 0;
ppst->tr_type = 0;
ppst->debug_lib = 0;
m_msp->nshow = 20;
ppst->max_repeat = 50;
m_msp->nohist = 1;
#if defined(PCOMPLIB)
m_msp->mshow = 20;
#else
#ifdef SHOW_HIST
m_msp->nohist = 0;
#endif
m_msp->mshow = 50;
#endif
m_msp->do_showbest = 1;
m_msp->ashow = -1;
m_msp->ashow_set = 0;
m_msp->nmlen = DEF_NMLEN;
m_msp->z_bits = 1;
m_msp->mshow_set = 0;
m_msp->mshow_min = 0;
m_msp->aln.llen = 60;
m_msp->aln.llcntx = 30;
m_msp->aln.llcntx_set = 0;
m_msp->e_low = 0.0;
m_msp->e_cut_set = 0;
m_msp->revcomp = 0;
m_msp->long_info = 0;
m_msp->ldb_info.maxn = 0;
m_msp->ldb_info.dupn = SEQDUP;
m_msp->dfile[0] = '\0';
m_msp->tname[0] = '\0';
m_msp->lname[0] = '\0';
m_msp->link_lname[0] = '\0';
m_msp->show_code = 0;
m_msp->aln.showall = 0;
m_msp->markx = 0;
m_msp->markx_list = NULL;
m_msp->align_done = 0;
m_msp->sq0off = m_msp->sq1off = 1;
strncpy(m_msp->sqnam,"aa",4);
strncpy(m_msp->sqtype,"protein",10);
m_msp->ann_flg = 0;
m_msp->ann_arr[0] = '\0';
m_msp->aa0a = NULL;
ppst->LK_set = 0;
ppst->e_cut = m_msp->e_cut = 10.0;
ppst->e_cut_r = ppst->e_cut / 10.0;
ppst->do_rep = 1;
ppst->zs_win = 0;
ppst->show_ident = 0;
ppst->zdb_size = -1;
ppst->zdb_size_set = 0;
ppst->dnaseq = SEQT_PROT; /* default is protein */
ppst->nt_align = 0;
ppst->other_info = NULL;
g_init_opts(m_msp, ppst);
f_initenv (m_msp, ppst, aa0);
if (argc == 1) {
show_help(m_msp->pgm_name, ppst->pgm_id);
}
if (strcmp(argv[1],"-help")==0) {
show_all_help(m_msp->pgm_name, ppst->pgm_id);
}
strncpy (optstring, g_optstring, sizeof (optstring));
strncat (optstring, f_optstring, sizeof (optstring));
while ((copt = getopt (argc, argv, optstring)) != EOF)
{
if (strchr (g_optstring, copt) != NULL)
{
switch (copt) { /* switches for all options */
case 'C':
sscanf(optarg,"%d",&m_msp->nmlen);
if (m_msp->nmlen > MAX_UID-1) m_msp->nmlen = MAX_UID-1;
break;
case 'D': ppst->debug_lib = 1;
break;
case 'e':
strncpy(m_msp->link_lname, optarg, MAX_LSTR);
break;
case 'F':
sscanf(optarg,"%lg",&m_msp->e_low);
m_msp->e_cut_set = 1;
break;
#if defined(PCOMPLIB) || !defined(SHOW_HIST)
case 'H':
m_msp->nohist = 0; break;
#else
case 'H':
m_msp->nohist = 1; break;
#endif
case 'i':
m_msp->revcomp = 1; break;
case 'I':
m_msp->quiet = 0; break;
case 'l':
strncpy(m_msp->flstr,optarg,MAX_FN);
m_msp->flstr[MAX_FN-1]='\0';
break;
case 'L':
m_msp->long_info = 1;
long_info_set = 1;
break;
case 'm':
pre_parse_markx(optarg, m_msp);
break;
case 'N':
sscanf(optarg,"%d",&m_msp->ldb_info.maxn);
break;
case 'o':
sscanf (optarg,"%ld %ld",&m_msp->sq0off,&m_msp->sq1off); break;
case 'O':
strncpy(m_msp->outfile,optarg,MAX_FN);
m_msp->outfile[MAX_FN-1]='\0';
break;
case 'q':
case 'Q':
m_msp->quiet = 1;
break;
case 'R':
strncpy (m_msp->dfile, optarg, MAX_FN);
m_msp->dfile[MAX_FN-1]='\0';
break;
case 'T':
#ifdef PCOMPLIB
if (strchr(optarg,'-') != NULL) {
sscanf(optarg,"%d-%d",&worker_1,&worker_n);
if (worker_1 > worker_n) {
worker_1 = worker_n = 0;
}
}
else
#endif
sscanf (optarg, "%d", &fa_max_workers);
if (fa_max_workers < 0) fa_max_workers=1;
break;
case 'v':
sscanf (optarg,"%d",&ppst->zs_win);
break;
case 'V':
strncpy(m_msp->ann_arr+1,optarg,MAX_FN-2);
m_msp->ann_arr[0]='\0';
m_msp->ann_arr[MAX_FN-2]='\0';
m_msp->ann_flg = 1;
add_ascii_ann(qascii, m_msp->ann_arr);
break;
/*
case 'V':
fprintf(stderr," -V option not currently supported in parallel\n");
break;
*/
case 'w':
sscanf (optarg,"%d",&m_msp->aln.llen);
if (m_msp->aln.llen < 10) m_msp->aln.llen = 10;
if (m_msp->aln.llen > 200) m_msp->aln.llen = 200;
if (!m_msp->aln.llcntx_set) m_msp->aln.llcntx = m_msp->aln.llen/2;
llen_set = 1;
break;
case 'Z':
sscanf(optarg,"%ld",&ppst->zdb_size);
ppst->zdb_size_set = 1;
break;
}
}
else if (strchr (f_optstring, copt))
f_getopt (copt, optarg, m_msp, ppst);
}
optind--;
f_lastenv (m_msp, ppst);
if (argc - optind < 3) return;
m_msp->tnamesize = sizeof (m_msp->tname);
if (argc - optind > 1) {strncpy (m_msp->tname, argv[optind + 1],MAX_FN);}
if (argc - optind > 2) {strncpy(m_msp->lname, argv[optind + 2],MAX_LSTR);}
f_getarg (argc, argv, optind, m_msp, ppst);
}
