/*===========================================================================*/
int main(int argc, char **argv) {
char *docname, *writename;
int mo_number = 0;
ghmm_cmodel ** smo;
ghmm_set_loglevel(5+1);
if(argc <= 1) {
printf("Usage: %s docname.smo docname.xml", argv[0]);
return(0);
}
docname = argv[1];
smo = ghmm_cmodel_read(docname, &mo_number);
printf("Models %d", mo_number);
/* simple test */
if (smo) {
writename = argv[2];
ghmm_cmodel_xml_write(smo, writename, mo_number);
}
return(0);
}
static int smix_hmm_run(int argc, char* argv[]) {
#define CUR_PROC "smix_hmm_run"
int k, exitcode = -1, smo_number, sqd_fields;
ghmm_cseq **sqd = NULL;
ghmm_cmodel **smo = NULL;
double **cp = NULL;
FILE *outfile = NULL;
/* read sequences and initial models */
sqd = ghmm_cseq_read(argv[1], &sqd_fields);
if (!sqd) {GHMM_LOG_QUEUED(LCONVERTED); goto STOP;}
if (sqd_fields > 1)
printf("Warning: Seq. File contains multiple Seq. Fields; use only the first one\n");
smo = ghmm_cmodel_read(argv[2], &smo_number);
if (!smo) {GHMM_LOG_QUEUED(LCONVERTED); goto STOP;}
/* open output file */
if(!(outfile = ighmm_mes_fopen(argv[3], "wt"))) {GHMM_LOG_QUEUED(LCONVERTED); goto STOP;}
/* matrix for component probs., */
cp = ighmm_cmatrix_alloc(sqd[0]->seq_number, smo_number);
if (!cp) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP;}
/* set last arg in ghmm_smixturehmm_init() :
1 = strict random partition; cp = 0/1
2. ghmm_smap_bayes from initial models
3. cp = 1 for best model, cp = 0 for other models
4. open
5. no start partition == equal cp for each model
*/
if (ghmm_smixturehmm_init(cp, sqd[0], smo, smo_number, 5) == -1) {
GHMM_LOG_QUEUED(LCONVERTED); goto STOP;
}
/* clustering */
if (ghmm_smixturehmm_cluster(outfile, cp, sqd[0], smo, smo_number) == -1) {
GHMM_LOG_QUEUED(LCONVERTED); goto STOP;
}
/* print trained models */
for (k = 0; k < smo_number; k++)
ghmm_cmodel_print(outfile, smo[k]);
if (outfile) fclose(outfile);
exitcode = 0;
STOP:
return exitcode;
# undef CUR_PROC
}
int main(int argc, char* argv[]) {
# define CUR_PROC "main"
#ifdef GHMM_OBSOLETE
int mo_number, smo_number;
#ifdef CMODEL_INCLUDED
int cmo_number;
#endif
int discrete = 0, smodelflag = 0;
int T, i, j;
ghmm_dmodel **mo = NULL;
#ifdef CMODEL_INCLUDED
cmodel **cmo = NULL;
#endif
ghmm_cmodel **smo = NULL;
double d;
/* double dangle, ddiff, s1, s2; */
if (argc != 5) {
printf("Usage: main <Model File> <discrete-flag> <T> <smodel flag>\n");
exit(1);
}
discrete = atoi(argv[2]);
T = atoi(argv[3]);
smodelflag = atoi(argv[4]);
ghmm_rng_init();
if (smodelflag) {
smo = ghmm_cmodel_read(argv[1], &smo_number);
if (!smo) {GHMM_LOG_QUEUED(LCONVERTED); return -1;}
if (smo_number < 2) {
printf("Need at least two HMMs to compare (read %d)\n", smo_number);
return -1;
}
for (i = 0; i < smo_number - 1; i++)
for (j = i + 1; j < smo_number; j++) {
printf("#----- mo[%d], mo[%d] \n", i , j);
/* syntax prob_dist: (smo1, smo2, total seqlen., symmetric, verbose) */
d = ghmm_cmodel_prob_distance(smo[i], smo[j], T, 1, 0);
printf("probdist = %f\n",d);
}
}
else if (discrete) {
mo = ghmm_dmodel_read(argv[1], &mo_number);
if (!mo) {GHMM_LOG_QUEUED(LCONVERTED); return -1;}
if (mo_number < 2) {
printf("Need at least two HMMs to compare\n");
return -1;
}
printf("#----- mo[0], mo[1] \n");
d = ghmm_dmodel_prob_distance(mo[0],mo[1], T, 0, 1);
printf("d=%f\n",d);
printf("#----- mo[1], mo[0] \n");
d = ghmm_dmodel_prob_distance(mo[1],mo[0], T, 0, 1);
printf("d=%f\n",d);
printf("#----- mo[0], mo[1] \n");
d = ghmm_dmodel_prob_distance(mo[0],mo[1], T, 0, 0);
printf("d=%f\n",d);
printf("#----- mo[1], mo[0] \n");
d = ghmm_dmodel_prob_distance(mo[1],mo[0], T, 0, 0);
printf("d=%f\n",d);
printf("#----- mo[0], mo[1] \n");
d = ghmm_dmodel_prob_distance(mo[0],mo[1], T, 1, 1);
printf("d=%f\n",d);
printf("#----- mo[0], mo[1] \n");
d = ghmm_dmodel_prob_distance(mo[0],mo[1], T, 1, 0);
printf("d=%f\n",d);
}
#ifdef CMODEL_INCLUDED
else {
cmo = cmodel_read(argv[1], &cmo_number);
if (!cmo) {GHMM_LOG_QUEUED(LCONVERTED); return -1;}
if (cmo_number < 2) {
printf("Need at least two CHMMs to compare\n");
return -1;
}
printf("#----- cmo[0], cmo[1] \n");
d = cmodel_prob_distance(cmo[0], cmo[1], T, 0, 1);
printf("d=%f\n",d);
printf("#----- cmo[1], cmo[0] \n");
d = cmodel_prob_distance(cmo[1], cmo[0], T, 0, 1);
printf("d=%f\n",d);
printf("#----- cmo[0], cmo[1] \n");
d = cmodel_prob_distance(cmo[0], cmo[1], T, 0, 0);
printf("d=%f\n",d);
printf("#----- cmo[1], cmo[0] \n");
d = cmodel_prob_distance(cmo[1], cmo[0], T, 0, 0);
printf("d=%f\n",d);
printf("#----- cmo[0], cmo[1] \n");
d = cmodel_prob_distance(cmo[0], cmo[1], T, 1, 1);
printf("d=%f\n",d);
printf("#----- cmo[0], cmo[1] \n");
d = cmodel_prob_distance(cmo[0], cmo[1], T, 1, 0);
printf("d=%f\n",d);
/* coemission likelihood */
printf("#----- cmo[0]/cmo[1] \n");
if (cmodel_coemission_likelihood(cmo[0], cmo[1], &d) == -1) d = -1;
printf("Coemission Likelihood = %e\n",d);
printf("#----- cmo[0]/cmo[0] \n");
if (cmodel_coemission_likelihood(cmo[0], cmo[0], &d) == -1) d = -1;
printf("Coemission Likelihood = %e\n",d);
printf("#----- cmo[1]/cmo[1] \n");
if (cmodel_coemission_likelihood(cmo[1], cmo[1], &d) == -1) d = -1;
printf("Coemission Likelihood = %e\n",d);
printf("#----- D_angle, D_diff, S1, S2\n");
cmodel_measures(cmo[0], cmo[1], &dangle, &ddiff, &s1, &s2);
printf("D_angle = %e\n", dangle);
printf("D_diff = %e\n", ddiff);
printf("S1 = %e\n", s1);
printf("S2 = %e\n", s2);
}
#endif /* CMODEL_INCLUDED*/
#else /* GHMM_OBSOLETE */
fprintf (stderr, "probdist is obsolete. If you need it rebuild the GHMM with \"GHMM_OBSOLETE\".\n");
#endif /* GHMM_OBSOLETE */
return 0;
}
