void get_args (int argc, char **argv, int *output_mode, struct mafFile **file, char **id,
struct MOTIF **motif, int *do_order, int *nrow, float *cutoff, int *misses_allowed)
{
int i;
if (argc < 5 || argc > 12)
fatalf (SYNTAX);
if (strcmp (argv[1], "-verbose") == 0)
*output_mode = VERBOSE;
else if (strcmp (argv[1], "-gala") == 0)
*output_mode = GALA;
else if (strcmp (argv[1], "-hgb") == 0)
*output_mode = HGB;
else
fatalf (SYNTAX);
*file = mafOpen (argv[2]);
strcpy (*id, argv[4]);
i = 5;
argc -= 5;
while (argc)
{
if (strcmp (argv[i], "-order") == 0)
*do_order = 1;
else if (strcmp (argv[i], "-nseq") == 0) {
i++;
argc--;
if (argc == 0)
fatal (SYNTAX);
*nrow = atoi (argv[i]);
if (*nrow < 2)
fatal ("Number of sequences must be at least 2.\n");
} else if (strcmp (argv[i], "-cut") == 0) {
i++;
argc--;
if (argc == 0)
fatal (SYNTAX);
*cutoff = atof (argv[i]);
if (*cutoff < 0.0 || *cutoff > 1.0)
fatal ("Cutoff value must be between 0 and 1.\n");
} else if (strcmp (argv[i], "-nm") == 0) {
i++;
argc--;
if (argc == 0)
fatal (SYNTAX);
*misses_allowed = atoi (argv[i]);
if (*misses_allowed < 0)
fatal ("Number of misses cannot be negative.\n");
} else
fatalf (SYNTAX);
argc--;
i++;
}
init_motif (motif, argv[3], *cutoff, *id);
}
void init(data *d) {
init_alph(&d->alph, d->a.alph_name);
init_motif(&d->m, d);
init_d_prior(&d->scorer.d_prior, d);
init_i_prior(&d->scorer.i_prior, d);
init_e_prior(&d->scorer.e_prior, d);
init_scores(d);
init_dp(d);
init_hit(d);
d->out = xfopen(d->a.out_file, "w");
}
