int run_file() {
Node *ptree;
AstNode *stree;
EmCodeObject *co;
EmObject *retval;
ptree = parse();
if (ptree) {
printtree(ptree);
stree = ast_from_ptree(ptree);
printstree(stree);
co = compile_ast_tree(stree);
printobj((EmObject *)co, stdout);
INCREF(&nulobj);
retval = run_codeobject(co, NULL, &nulobj);
if (retval)
DECREF(retval);
freetree(ptree);
freestree(stree);
}
fclose(source.fp);
return 1;
}
int run_prompt() {
Node *ptree;
AstNode *stree;
EmCodeObject *co;
Environment *env;
EmObject *retval;
env = newenv(vm->topenv);
while (1) {
ptree = parse();
if (ptree) {
if (ptree->type != MAGIC_COMMAND) {
// printtree(ptree);
stree = ast_from_ptree(ptree);
// printstree(stree);
co = compile_ast_tree(stree);
INCREF(&nulobj);
retval = run_codeobject(co, env, &nulobj);
if (retval)
DECREF(retval);
vm_reset_for_prompt();
freetree(ptree);
freestree(stree);
} else { // MAGIC_COMMAND
printf("got magic command %d\n", CHILD(ptree,0)->type);
if (NCH(ptree) == 2) {
printf("magic command arg = %s\n",
CHILD(ptree,1)->lexeme);
}
if (CHILD(ptree,0)->type == MCA_EXIT) {
freetree(ptree); // release memory before exit
break;
}
// Always release memory of parse tree
freetree(ptree);
}
}
}
env_free(env);
return 1;
}
Sint procmaxmatches(MMcallinfo *mmcallinfo,Multiseq *subjectmultiseq)
{
Matchprocessinfo matchprocessinfo;
Uint filenum, filelen;
Sint retcode;
Uchar *filecontent;
double start, finish;
/*fprintf(stderr,"# construct suffix tree for sequence of length %lu\n",
(Showuint) subjectmultiseq->totallength);
fprintf(stderr,"# (maximum reference length is %lu)\n",
(Showuint) getmaxtextlenstree());
fprintf(stderr,"# (maximum query length is %lu)\n",
(Showuint) ~((Uint)0));*/
start = omp_get_wtime();
if(constructprogressstree (&matchprocessinfo.stree,
subjectmultiseq->sequence,
subjectmultiseq->totallength,
NULL,
NULL,
NULL) != 0)
{
return -1;
}
finish = omp_get_wtime();
/*fprintf(stderr,"# CONSTRUCTIONTIME %s %s %.2f\n",
&mmcallinfo->program[0],&mmcallinfo->subjectfile[0],
getruntime());*/
matchprocessinfo.subjectmultiseq = subjectmultiseq;
matchprocessinfo.minmatchlength = mmcallinfo->minmatchlength;
matchprocessinfo.showstring = mmcallinfo->showstring;
matchprocessinfo.showsequencelengths = mmcallinfo->showsequencelengths;
matchprocessinfo.showreversepositions = mmcallinfo->showreversepositions;
matchprocessinfo.forward = mmcallinfo->forward;
matchprocessinfo.fourcolumn = mmcallinfo->fourcolumn;
matchprocessinfo.cmum = mmcallinfo->cmum;
matchprocessinfo.cmumcand = mmcallinfo->cmumcand;
matchprocessinfo.reversecomplement = mmcallinfo->reversecomplement;
matchprocessinfo.chunks = mmcallinfo->chunks;
if(mmcallinfo->cmum)
{
INITARRAY(&matchprocessinfo.mumcandtab,MUMcandidate);
}
retcode = getmaxdesclen(subjectmultiseq);
if(retcode < 0)
{
return -2;
}
matchprocessinfo.maxdesclength = (Uint) retcode;
for(filenum=0; filenum < mmcallinfo->numofqueryfiles; filenum++)
{
filecontent = CREATEMEMORYMAP (mmcallinfo->queryfilelist[filenum],
True,
&filelen);
if (filecontent == NULL || filelen == 0)
{
ERROR2("cannot open file \"%s\" or file \"%s\" is empty",
mmcallinfo->queryfilelist[filenum],
mmcallinfo->queryfilelist[filenum]);
return -3;
}
if (scanmultiplefastafile (&matchprocessinfo.querymultiseq,
mmcallinfo->queryfilelist[filenum],
mmcallinfo->matchnucleotidesonly
? MMREPLACEMENTCHARQUERY
: 0,
filecontent, filelen) != 0)
{
return -4;
}
/*fprintf(stderr,
"# matching query-file \"%s\"\n# against subject-file \"%s\"\n",
mmcallinfo->queryfilelist[filenum],
mmcallinfo->subjectfile);*/
if (overallsequences (False,
&matchprocessinfo.querymultiseq,
(void *) &matchprocessinfo,
findmaxmatchesonbothstrands) != 0)
{
return -5;
}
freemultiseq(&matchprocessinfo.querymultiseq);
}
if(mmcallinfo->cmum)
{
FREEARRAY(&matchprocessinfo.mumcandtab,MUMcandidate);
}
freestree (&matchprocessinfo.stree);
fprintf(stdout,"ST=%f,",(double) (finish-start));
return 0;
}
