void
FreeTophits(struct tophit_s *h)
{
int pos;
for (pos = 0; pos < h->num; pos++)
{
if (h->unsrt[pos].ali != NULL) FreeFancyAli(h->unsrt[pos].ali);
if (h->unsrt[pos].name != NULL) free(h->unsrt[pos].name);
if (h->unsrt[pos].desc != NULL) free(h->unsrt[pos].desc);
}
free(h->unsrt);
if (h->hit != NULL) free(h->hit);
free(h);
}
int
main(int argc, char **argv)
{
char *cmfile;
ESL_ALPHABET *abc;
char *seqfile;
ESL_SQFILE *sqfp;
int format;
CM_FILE *cmfp;
CM_t *cm;
ESL_SQ *seq;
float sc, rev_sc;
Parsetree_t *tr;
Fancyali_t *fali;
Fancyali_t *rev_fali;
int do_local;
/* int status; */
/* char *optname; */
/* char *optarg; */
int optind;
int status;
char errbuf[eslERRBUFSIZE];
cmfile = seqfile = NULL;
abc = NULL;
sqfp = NULL;
cmfp = NULL;
cm = NULL;
seq = NULL;
tr = NULL;
fali = NULL;
rev_fali = NULL;
format = eslSQFILE_UNKNOWN;
do_local = TRUE;
/* Should process options, but for now assume none and set optind */
optind = 1;
if ( argc - optind != 2 ) cm_Die("Incorrect number of arguments\n");
cmfile = argv[optind++];
seqfile = argv[optind++];
if((status = cm_file_Open(cmfile, NULL, FALSE, &cmfp, errbuf)) != eslOK)
cm_Die("Failed to open covariance model save file\n");
if ((status = cm_file_Read(cmfp, TRUE, &abc, &cm)) != eslOK)
cm_Die("Failed to read a CM from cm file\n");
if (cm == NULL)
cm_Die("CM file empty?\n");
cm_file_Close(cmfp);
if ( esl_sqfile_Open(seqfile, format, NULL, &sqfp) != eslOK )
cm_Die("Failed to open sequence database file\n");
if (do_local) cm->config_opts |= CM_CONFIG_LOCAL;
if((status = cm_Configure(cm, errbuf, -1)) != eslOK) cm_Die(errbuf);
/*SetMarginalScores_reproduce_bug_i27(cm);*/
seq = esl_sq_Create();
while ( esl_sqio_Read(sqfp, seq) == eslOK )
{
if (seq->n == 0) continue;
int i0 = 1;
int j0 = seq->n;
if (seq->dsq == NULL)
esl_sq_Digitize(abc, seq);
sc = TrCYK_DnC(cm, seq->dsq, seq->n, 0, i0, j0, PLI_PASS_5P_AND_3P_ANY, TRUE, &tr); /* TRUE: reproduce v1.0 behavior */
/* sc = TrCYK_Inside(cm, seq->dsq, seq->n, 0, i0, j0, PLI_PASS_5P_AND_3P_ANY, TRUE, FALSE, &tr); */
fali = CreateFancyAli(cm->abc, tr, cm, cm->cmcons, seq->dsq, FALSE, NULL);
/* float sc, struct_sc;
* ParsetreeScore(cm, NULL, NULL, tr, seq->dsq, FALSE, &sc, &struct_sc, NULL, NULL, NULL);
* printf("Parsetree score: %.4f\n", sc);
* ParsetreeDump(stdout, tr, cm, seq->dsq);
*/
FreeParsetree(tr);
revcomp(abc, seq, seq);
rev_sc = TrCYK_DnC(cm,seq->dsq, seq->n, 0, i0, j0, PLI_PASS_5P_AND_3P_ANY, TRUE, &tr); /* TRUE: reproduce v1.0 behavior */
rev_fali = CreateFancyAli(cm->abc, tr, cm, cm->cmcons,seq->dsq, FALSE, NULL);
/*ParsetreeDump(stdout, tr, cm, seq->dsq);*/
FreeParsetree(tr);
if (sc > rev_sc)
{
printf("sequence: %s\n", seq->name);
printf("score: %.2f\n",sc);
PrintFancyAli(stdout, fali, 0, FALSE, FALSE, 60);
}
else
{
printf("sequence: %s (reversed)\n", seq->name);
printf("score: %.2f\n",rev_sc);
PrintFancyAli(stdout, fali, seq->n, TRUE, FALSE, 60);
}
FreeFancyAli(fali);
FreeFancyAli(rev_fali);
esl_sq_Destroy(seq);
seq = esl_sq_Create();
}
esl_sq_Destroy(seq);
FreeCM(cm);
esl_sqfile_Close(sqfp);
return EXIT_SUCCESS;
}
