void mark_global(VARIABLE *v)
{
if (v == NULL)
return;
mark_global(v->next);
v->global = 1;
}
static void
mark_stacks(void)
{
mark_registers();
mark_trail();
mark_local();
mark_global();
}
static void
mark_stacks(USES_REGS1)
{
mark_registers(PASS_REGS1);
mark_trail(PASS_REGS1);
mark_local(PASS_REGS1);
mark_global(PASS_REGS1);
}
SERVICE *makeSERVICE(HTML *htmls, SCHEMA *schemas,
VARIABLE *variables, FUNCTION *functions,
SESSION *sessions)
{
SERVICE *s = NEW(SERVICE);
s->htmls = htmls;
s->schemas = schemas;
s->variables = variables;
mark_global(s->variables);
s->functions = functions;
s->sessions = sessions;
return s;
}
/*============================*/
int main (int argc, char *argv[]) {
int tmp;
char *line;
loc_min *LM;
int *tm;
int i;
char signal[100]="", what[100]="", stuff[100]="";
/* Parse command line */
program_name = argv[0];
opt.kT = -300;
opt.MOVESET = "";
opt.minh = 0.0000001;
opt.label = 0; /* normally, use numbers for minima */
GRAPH = NULL;
/* Try to parse head to determine graph-type */
decode_switches (argc, argv);
if (args_info.inputs_num > 0) {
opt.INFILE = fopen(args_info.inputs[0], "r");
if (opt.INFILE==NULL) nrerror("can't open file");
} else {
opt.INFILE = stdin;
}
line = get_line(opt.INFILE);
if (line == NULL) {
fprintf(stderr,"Error in input file\n");
exit(123);
}
opt.seq = (char *) space(strlen(line) + 1);
sscanf(line,"%s %d %99s %99s %99s", opt.seq, &tmp, signal, what, stuff);
if(strcmp(stuff, "\0")!=0 && strncmp(what, "Q", 1)==0) { /* lattice proteins*/
memset(opt.seq, 0, strlen(line)+1);
strcpy(opt.seq, stuff);
}
if ((!opt.poset)&&(strcmp(signal,"::")!=0)) {
int r, dim;
/* in this case we have a poset file !!!! */
r=sscanf(signal,"P:%d",&dim);
if(r<1) {
fprintf(stderr,
"Warning: obscure headline in input file\n");
dim = 0;
}
if(dim>0) opt.poset = dim;
}
if (opt.poset) { /* in this case we have a poset file !!!! */
fprintf(stderr,
"!!! Input data are a poset with %d objective functions\n",
opt.poset);
/* we have a SECIS design file */
if ( ((GRAPH != NULL) && (strstr(GRAPH, "SECIS") != NULL))
||(strncmp(what, "SECIS", 5) == 0) )
{
#if HAVE_SECIS_EXTENSION
int len, max_m, min_as;
char *sec_structure, *protein_sequence;
if (sscanf(what,"SECIS,%d,%d", &max_m, &min_as) < 2) {
fprintf(stderr,
"Error in input format for SECIS design !"
"expected format: SECIS,INT,INT\n"
"got: `%s'",
what);
exit(EXIT_FAILURE);
}
free(line);
line = get_line(opt.INFILE);
len = strlen(line);
sec_structure = (char*)calloc(len+1, sizeof(char));
protein_sequence = (char*)calloc(len+1, sizeof(char));
sscanf(line,"%s %s", sec_structure, protein_sequence);
if (opt.want_verbose)
fprintf(stderr,
"\nGraph is SECIS design with the following parameters:\n"
"Structure: %s\n"
"Constraints: %s\n"
"Protein sequence: %s\n"
"Max. number of mutations : %d\n"
"Min. alignment score (aa): %d\n\n",
sec_structure,
opt.seq,
protein_sequence,
max_m,
min_as);
initialize_SECIS(opt.seq, sec_structure, protein_sequence,
max_m, min_as);
free(sec_structure);
free(protein_sequence);
#else
fprintf(stderr,
"You need to reconfigure barriers with the --with-secis"
" option\nto use barriers SECIS design extension\n");
exit(EXIT_FAILURE);
#endif
}
}
free(line);
if (GRAPH==NULL)
if(strlen(what)) GRAPH = what;
if (GRAPH==NULL) GRAPH="RNA";
opt.GRAPH=GRAPH;
LM = barriers(opt);
if (opt.INFILE != stdin) fclose(opt.INFILE);
tm = make_truemin(LM);
if(opt.poset) mark_global(LM);
print_results(LM,tm,opt.seq);
fflush(stdout);
if (!opt.want_quiet) ps_tree(LM,tm,0);
if (opt.rates || opt.microrates) {
compute_rates(tm,opt.seq);
if (!opt.want_quiet) ps_tree(LM,tm,1);
print_rates(tm[0], "rates.out");
}
if (opt.poset) mark_global(LM);
for (i = 0; i < args_info.path_given; ++i) {
int L1, L2;
sscanf(args_info.path_arg[i], "%d=%d", &L1, &L2);
if ((L1>0) && (L2>0)) {
FILE *PATH = NULL;
char tmp[30];
path_entry *path;
path = backtrack_path(L1, L2, LM, tm);
(void) sprintf(tmp, "path.%03d.%03d.txt", L1, L2);
PATH = fopen (tmp, "w");
if (PATH == NULL) nrerror("couldn't open path file");
print_path(PATH, path, tm);
/* fprintf(stderr, "%llu %llu\n", 0, MAXIMUM); */
fclose (PATH);
fprintf (stderr, "wrote file %s\n", tmp);
free (path);
}
}
/* memory cleanup */
free(opt.seq);
free(LM);
free(tm);
#if WITH_DMALLOC
kill_hash(); /* freeing the hash takes unacceptably long */
#endif
cmdline_parser_free(&args_info);
exit(0);
}