int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO);
ESL_SQ *sq = esl_sq_CreateDigital(abc);
ESL_SQFILE *sqfp = NULL;
ESL_HMM *hmm = create_test_hmm(abc);
ESL_HMM *bg = create_null_hmm(abc);
ESL_HMX *hmx = esl_hmx_Create(400, hmm->M);
int format = eslSQFILE_UNKNOWN;
char *seqfile = esl_opt_GetArg(go, 1);
float fwdsc, nullsc;
int status;
status = esl_sqfile_OpenDigital(abc, seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) esl_fatal("No such file.");
else if (status == eslEFORMAT) esl_fatal("Format unrecognized.");
else if (status != eslOK) esl_fatal("Open failed, code %d.", status);
while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
{
esl_hmx_GrowTo(hmx, sq->n, hmm->M);
esl_hmm_Forward(sq->dsq, sq->n, hmm, hmx, &fwdsc);
esl_hmm_Forward(sq->dsq, sq->n, bg, hmx, &nullsc);
printf("%-16s %5d %11.4f %8.4f %11.4f %8.4f %11.4f %8.4f\n", sq->name, (int) sq->n,
fwdsc * eslCONST_LOG2R, (fwdsc * eslCONST_LOG2R) / sq->n,
nullsc * eslCONST_LOG2R, (nullsc * eslCONST_LOG2R) / sq->n,
(fwdsc - nullsc) * eslCONST_LOG2R, (fwdsc-nullsc) * eslCONST_LOG2R / sq->n);
esl_sq_Reuse(sq);
}
if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s)\n%s\n",
sqfp->filename, sqfp->get_error(sqfp));
else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
status, sqfp->filename);
esl_sqfile_Close(sqfp);
esl_sq_Destroy(sq);
esl_hmm_Destroy(hmm);
esl_hmm_Destroy(bg);
esl_hmx_Destroy(hmx);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
/* Function: p7_bg_Destroy()
* Incept: SRE, Fri Jan 12 14:04:30 2007 [Janelia]
*
* Purpose: Frees a <P7_BG> object.
*
* Returns: (void)
*
* Xref: STL11/125.
*/
void
p7_bg_Destroy(P7_BG *bg)
{
if (bg != NULL) {
if (bg->f != NULL) free(bg->f);
if (bg->fhmm != NULL) esl_hmm_Destroy(bg->fhmm);
free(bg);
}
return;
}
/* Function: esl_hmm_Create()
* Synopsis: Allocates a new HMM.
*
* Purpose: Allocates a new HMM of <M> states for
* generating or modeling strings in the
* alphabet <abc>.
*
* Returns: a pointer to the new HMM.
*
* Throws: <NULL> on allocation failure.
*/
ESL_HMM *
esl_hmm_Create(const ESL_ALPHABET *abc, int M)
{
ESL_HMM *hmm = NULL;
int k,x;
int status;
ESL_ALLOC(hmm, sizeof(ESL_HMM));
hmm->t = NULL;
hmm->e = NULL;
hmm->eo = NULL;
hmm->pi = NULL;
ESL_ALLOC(hmm->t, sizeof(float *) * M); hmm->t[0] = NULL;
ESL_ALLOC(hmm->e, sizeof(float *) * M); hmm->e[0] = NULL;
ESL_ALLOC(hmm->eo, sizeof(float *) * abc->Kp); hmm->eo[0] = NULL;
ESL_ALLOC(hmm->pi, sizeof(float) * (M+1)); // initial transition to state M means a L=0 sequence
ESL_ALLOC(hmm->t[0], sizeof(float) * M * (M+1)); // state M is the implicit end state
ESL_ALLOC(hmm->e[0], sizeof(float) * M * abc->K);
ESL_ALLOC(hmm->eo[0], sizeof(float) * abc->Kp * M);
for (k = 1; k < M; k++)
{
hmm->t[k] = hmm->t[0] + k*(M+1);
hmm->e[k] = hmm->e[0] + k*abc->K;
}
for (x = 1; x < abc->Kp; x++)
hmm->eo[x] = hmm->eo[0] + x*M;
hmm->M = M;
hmm->K = abc->K;
hmm->abc = abc;
return hmm;
ERROR:
esl_hmm_Destroy(hmm);
return NULL;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage);
ESL_RANDOMNESS *r = esl_randomness_Create(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET *abc = NULL;
ESL_HMM *hmm = NULL;
ESL_DSQ *dsq = NULL;
int *path = NULL;
ESL_HMX *fwd = NULL;
ESL_HMX *bck = NULL;
ESL_HMX *pp = NULL;
int be_verbose = esl_opt_GetBoolean(go, "-v");
float fsc, bsc;
int L;
int i;
float fsum, bsum;
make_occasionally_dishonest_casino(&hmm, &abc);
esl_hmm_Emit(r, hmm, &dsq, &path, &L);
fwd = esl_hmx_Create(L, hmm->M);
bck = esl_hmx_Create(L, hmm->M);
pp = esl_hmx_Create(L, hmm->M);
esl_hmm_Forward (dsq, L, hmm, fwd, &fsc);
esl_hmm_Backward(dsq, L, hmm, bck, &bsc);
esl_hmm_PosteriorDecoding(dsq, L, hmm, fwd, bck, pp);
fsum = 0.0;
bsum = bsc;
fsum += fwd->sc[0];
if (be_verbose) printf("%4d %c %s %8.3f %8.3f\n", 0, '-', "--", fwd->sc[0], bck->sc[0]);
bsum -= bck->sc[0];
for (i = 1; i <= L; i++)
{
fsum += fwd->sc[i];
if (be_verbose)
printf("%4d %c %s %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n",
i, abc->sym[dsq[i]], path[i] == 0 ? "F " : " L",
fwd->sc[i], bck->sc[i],
fsum, bsum, fsum+bsum,
pp->dp[i][0], pp->dp[i][1]);
bsum -= fwd->sc[i];
}
if (be_verbose) {
printf("%4d %c %s %8.3f %8.3f\n", 0, '-', "--", fwd->sc[L+1], bck->sc[L+1]);
printf("Forward score = %f\n", fsc);
printf("Backward score = %f\n", bsc);
}
free(path);
free(dsq);
esl_hmx_Destroy(pp);
esl_hmx_Destroy(bck);
esl_hmx_Destroy(fwd);
esl_alphabet_Destroy(abc);
esl_hmm_Destroy(hmm);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return 0;
}
