int
main ()
{
char c;
char *line, *buffer, *tmp, *x;
int i, linelen, nothree;
long buflen, seqlen;
line = malloc (256);
if (!line)
return -1;
seqlen = 0;
nothree = 1;
while (nothree && fgets (line, 255, stdin))
if (line[0] == '>' && line[1] == 'T' && line[2] == 'H')
nothree = 0;
free (line);
buflen = 10240;
buffer = malloc (buflen + 1);
if (!buffer)
return -1;
x = buffer;
while (fgets (x, 255, stdin))
{
linelen = strlen (x);
if (linelen)
{
if (x[linelen - 1] == '\n')
linelen--;
c = x[0];
if (c == '>')
break;
else if (c != ';')
{
seqlen = seqlen + linelen;
if (seqlen + 512 >= buflen)
{
buflen = buflen + 10240;
tmp = realloc (buffer, buflen + 1);
if (tmp == NULL)
return -1;
buffer = tmp;
x = &(buffer[seqlen]);
}
else
x = &(x[linelen]);
x[0] = 0;
}
}
}
for (i = 0; i < seqlen; i++)
buffer[i] = toupper (buffer[i]);
write_frequencies (1, buffer, seqlen);
write_frequencies (2, buffer, seqlen);
write_count ("GGT", buffer, seqlen);
write_count ("GGTA", buffer, seqlen);
write_count ("GGTATT", buffer, seqlen);
write_count ("GGTATTTTAATT", buffer, seqlen);
write_count ("GGTATTTTAATTTATAGT", buffer, seqlen);
free (buffer);
return 0;
}
int
main (int argc, char **argv)
{
struct bloch_sim *b = malloc(sizeof(*b));
int option = 0;
realtype p_0 = 0.0;
realtype p_1 = 0.0;
int num_cells = 9;
int freq_write_flag = 0;
char *freq_file_str;
int env_write_flag = 0;
char *env_file_str;
// int param_write_flag;
while ((option = getopt(argc, argv,"l:q:h:e:c:")) != -1)
{
switch (option)
{
case 'l' :
p_0 = strtod(optarg, NULL);
break;
case 'q' :
p_1 = strtod(optarg, NULL);
break;
case 'h' :
freq_write_flag = 1;
freq_file_str = optarg;
break;
case 'e' :
env_write_flag = 1;
env_file_str = optarg;
break;
case 'c':
num_cells = atoi(optarg);
default:
//print_usage();
break;
}
}
initialize_bloch(b, p_0, p_1, num_cells);
simulate_nmr_pulse(b);
if (freq_write_flag)
{
FILE *freq_file = fopen(freq_file_str, "w");
if (freq_file == NULL) {
fprintf(stderr, "ERROR: failed to open frequency output file!\n");
exit(1);
}
write_frequencies(b, freq_file);
fclose(freq_file);
}
if (env_write_flag)
{
FILE *env_file = fopen(env_file_str, "w");
if (env_file == NULL) {
fprintf(stderr, "ERROR: failed to open envelope output file!\n");
exit(1);
}
write_envelope(b, env_file);
fclose(env_file);
}
free_bloch(b);
return 0;
}