ESL_HMX *
esl_hmx_Create(int allocL, int allocM)
{
ESL_HMX *mx = NULL;
int i;
int status;
ESL_ALLOC(mx, sizeof(ESL_HMX));
mx->dp_mem = NULL;
mx->dp = NULL;
mx->sc = NULL;
ESL_ALLOC(mx->dp_mem, sizeof(float) * (allocL+1) * allocM);
mx->ncells = (allocL+1) * allocM;
ESL_ALLOC(mx->dp, sizeof (float *) * (allocL+1));
ESL_ALLOC(mx->sc, sizeof (float) * (allocL+2));
mx->allocR = allocL+1;
for (i = 0; i <= allocL; i++)
mx->dp[i] = mx->dp_mem + i*allocM;
mx->validR = allocL+1;
mx->allocM = allocM;
mx->L = 0;
mx->M = 0;
return mx;
ERROR:
esl_hmx_Destroy(mx);
return NULL;
}
/* Function: p7_bg_FilterScore()
* Synopsis: Calculates the filter null model score.
* Incept: SRE, Thu Aug 28 08:52:53 2008 [Janelia]
*
* Purpose: Calculates the filter null model <bg> score for sequence
* <dsq> of length <L>, and return it in
* <*ret_sc>.
*
* The score is calculated as an HMM Forward score using
* the two-state filter null model. It is a log-odds ratio,
* relative to the iid background frequencies, in nats:
* same as main model Forward scores.
*
* The filter null model has no length distribution of its
* own; the same geometric length distribution (controlled
* by <bg->p1>) that the null1 model uses is imposed.
*/
int
p7_bg_FilterScore(P7_BG *bg, ESL_DSQ *dsq, int L, float *ret_sc)
{
ESL_HMX *hmx = esl_hmx_Create(L, bg->fhmm->M); /* optimization target: this can be a 2-row matrix, and it can be stored in <bg>. */
float nullsc; /* (or it could be passed in as an arg, but for sure it shouldn't be alloc'ed here */
esl_hmm_Forward(dsq, L, bg->fhmm, hmx, &nullsc);
/* impose the length distribution */
*ret_sc = nullsc + (float) L * logf(bg->p1) + logf(1.-bg->p1);
esl_hmx_Destroy(hmx);
return eslOK;
}
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;
}
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;
}
