int
rl_alphabetic (int c)
{
if (ALPHABETIC (c))
return (1);
return (_rl_allow_pathname_alphabetic_chars &&
strchr (pathname_alphabetic_chars, c) != NULL);
}
int match( const char *rna, const rna_t *mol, int t, int j )
/* Determine whether (t,j) is a valid base pair. */
{
char a = rna[t], b = rna[j];
const cell_t *right = &mol->opt[t+1][j-1];
/* no sharp-turn condition */
int r = right->score == 0 ||
(right->a - t == 1 && j - right->b == 1) ||
(right->a - t > LOOP && j - right->b > LOOP);
/* pair condition */
if (NUCLEOTIDE(a) && NUCLEOTIDE(b))
return r && (
(a == 'A' && b == 'U') ||
(a == 'U' && b == 'A') ||
(a == 'G' && b == 'C') ||
(a == 'C' && b == 'G'));
/* If not nucleotide, but alphabetic, match. Otherwise, don't match. */
else
return r && ALPHABETIC(a) && ALPHABETIC(b);
}
int parse_options( param_t &options, int argc, const char **argv )
/* Parse command line options and return a status, informing the up stream
* if the parameters weren't inputted correctly. */
{
options.shrink_factor = options.low = options.high = options.erode = options.dilate = -1;
options.prefix[0] = '\0';
for (int i = 1; i < argc; i++)
{
/* binary threshold */
if (strcmp(argv[i], "-t") == 0 && (argc - i) > 2) {
if (!NUMERIC(argv[i+1][0]) || !NUMERIC(argv[i+2][0]))
return 0;
options.low = atoi(argv[++i]);
options.high = atoi(argv[++i]);
if (options.low < 0 || options.low > options.high || options.high > 255)
return 0;
}
/* binary morpholoy */
else if (strcmp(argv[i], "-m") == 0 && (argc - i) > 2) {
if (!NUMERIC(argv[i+1][0]) || !NUMERIC(argv[i+2][0]))
return 0;
options.erode = atoi(argv[++i]);
options.dilate = atoi(argv[++i]);
if (options.erode < 0 || options.dilate < 0)
return 0;
if (options.low == -1) {
options.low = 40;
options.high = 60;
}
}
/* output file prefix */
else if (strcmp(argv[i], "-f") == 0 && (argc - i) > 1) {
i++;
for (int j = 0; j < strlen(argv[i]); j++) {
if (!ALPHABETIC(argv[i][j]))
return 0;
}
strcpy(options.prefix, argv[i]);
}
/* shrink factor */
else if (strcmp(argv[i], "-s") == 0 && (argc - i) > 1) {
options.shrink_factor = atoi(argv[++i]);
if (options.shrink_factor < 1)
return 0;
}
else
return 0;
}
if (options.shrink_factor < 0)
options.shrink_factor = 1;
if (options.prefix[0] == '\0')
strcpy(options.prefix, "test");
return 1;
} // parse_options()
