int
main(int argc, char **argv)
{
char *hmmfile = argv[1]; /* name of HMM file to read one HMM from */
ESL_ALPHABET *abc = NULL; /* sequence alphabet */
ESL_RANDOMNESS *r = NULL; /* source of randomness */
P7_HMMFILE *hfp = NULL; /* open hmmfile */
P7_HMM *hmm = NULL; /* HMM to emit from */
P7_PROFILE *gm = NULL; /* profile HMM (scores) */
P7_BG *bg = NULL; /* null model */
P7_TRACE *tr = NULL; /* sampled trace */
ESL_SQ *sq = NULL; /* sampled digital sequence */
int n = 1000;
int counts[p7T_NSTATETYPES];
int i;
float sc;
float nullsc;
double bitscore;
r = esl_randomness_CreateFast(0);
tr = p7_trace_Create();
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("failed to open %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("failed to read HMM");
sq = esl_sq_CreateDigital(abc);
bg = p7_bg_Create(abc);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
for (i = 0; i < n; i++)
{
p7_ProfileEmit(r, hmm, gm, bg, sq, tr);
p7_trace_GetStateUseCounts(tr, counts);
p7_ReconfigLength(gm, sq->n);
p7_bg_SetLength(bg, sq->n);
p7_trace_Score(tr, sq->dsq, gm, &sc);
p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
bitscore = (sc - nullsc)/ eslCONST_LOG2;
printf("%d %8.4f\n",
counts[p7T_M] + (counts[p7T_I] + counts[p7T_D])/2,
bitscore);
}
p7_profile_Destroy(gm);
esl_sq_Destroy(sq);
p7_trace_Destroy(tr);
esl_randomness_Destroy(r);
esl_alphabet_Destroy(abc);
p7_hmmfile_Close(hfp);
p7_hmm_Destroy(hmm);
return eslOK;
}
/* process_workunit()
*
* This is the routine that actually does the work.
*
* A work unit consists of one HMM, <hmm>.
* The result is the <scores> array, which contains an array of N scores;
* caller provides this memory.
* How those scores are generated is controlled by the application configuration in <cfg>.
*/
static int
process_workunit(ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf, P7_HMM *hmm, double *scores, int *alilens)
{
int L = esl_opt_GetInteger(go, "-L");
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_REFMX *rmx = NULL;
P7_CHECKPTMX *cx = NULL;
P7_FILTERMX *fx = NULL;
P7_TRACE *tr = NULL;
ESL_DSQ *dsq = NULL;
int i;
int scounts[p7T_NSTATETYPES]; /* state usage counts from a trace */
float sc;
float nullsc;
int status;
P7_HARDWARE *hw;
if ((hw = p7_hardware_Create ()) == NULL) p7_Fail("Couldn't get HW information data structure");
/* Optionally set a custom background, determined by model composition;
* an experimental hack.
*/
if (esl_opt_GetBoolean(go, "--bgcomp"))
{
float *p = NULL;
float KL;
p7_hmm_CompositionKLDist(hmm, cfg->bg, &KL, &p);
esl_vec_FCopy(p, cfg->abc->K, cfg->bg->f);
}
/* Create and configure our generic profile, as requested */
gm = p7_profile_Create(hmm->M, cfg->abc);
if (esl_opt_GetBoolean(go, "--multi"))
{
if (esl_opt_GetBoolean(go, "--dual")) { p7_profile_Config (gm, hmm, cfg->bg); }
else if (esl_opt_GetBoolean(go, "--local")) { p7_profile_ConfigLocal (gm, hmm, cfg->bg, L); }
else if (esl_opt_GetBoolean(go, "--glocal")) { p7_profile_ConfigGlocal(gm, hmm, cfg->bg, L); }
}
else if (esl_opt_GetBoolean(go, "--uni"))
{
if (esl_opt_GetBoolean(go, "--dual")) { p7_profile_ConfigCustom (gm, hmm, cfg->bg, L, 0.0, 0.5); }
else if (esl_opt_GetBoolean(go, "--local")) { p7_profile_ConfigUnilocal (gm, hmm, cfg->bg, L); }
else if (esl_opt_GetBoolean(go, "--glocal")) { p7_profile_ConfigUniglocal(gm, hmm, cfg->bg, L); }
}
p7_profile_SetLength(gm, L);
p7_bg_SetLength(cfg->bg, L);
if (esl_opt_GetBoolean(go, "--x-no-lengthmodel")) elide_length_model(gm, cfg->bg);
/* Allocate DP matrix for <gm>.
*/
rmx = p7_refmx_Create(gm->M, L);
/* Create and configure the vectorized profile, if needed;
* and allocate its DP matrix
*/
if (esl_opt_GetBoolean(go, "--vector"))
{
om = p7_oprofile_Create(gm->M, cfg->abc, om->simd);
p7_oprofile_Convert(gm, om);
cx = p7_checkptmx_Create(gm->M, L, ESL_MBYTES(32), om->simd);
fx = p7_filtermx_Create(gm->M, om->simd);
}
/* Remaining allocation */
ESL_ALLOC(dsq, sizeof(ESL_DSQ) * (L+2));
tr = p7_trace_Create();
/* Collect scores from N random sequences of length L */
for (i = 0; i < cfg->N; i++)
{
esl_rsq_xfIID(cfg->r, cfg->bg->f, cfg->abc->K, L, dsq);
sc = eslINFINITY;
/* Vectorized implementations of Viterbi, MSV may overflow.
* In this case, they'll leave sc=eslINFINITY.
* Then we fail over to the nonvector "generic" implementation.
* That's why this next block isn't an if/else.
*/
if (esl_opt_GetBoolean(go, "--vector"))
{
if (esl_opt_GetBoolean(go, "--vit")) p7_ViterbiFilter(dsq, L, om, fx, &sc);
else if (esl_opt_GetBoolean(go, "--fwd")) p7_ForwardFilter(dsq, L, om, cx, &sc);
else if (esl_opt_GetBoolean(go, "--msv")) p7_MSVFilter (dsq, L, om, fx, &sc);
}
/* If we tried a vector calculation above but it overflowed,
* or if we're to do --generic DP calculations, sc==eslINFINITY now;
* hence the if condition here:
*/
if (sc == eslINFINITY)
{
if (esl_opt_GetBoolean(go, "--fwd")) p7_ReferenceForward(dsq, L, gm, rmx, &sc); /* any mode: dual,local,glocal; gm's config takes care of this */
else if (esl_opt_GetBoolean(go, "--vit")) p7_ReferenceViterbi(dsq, L, gm, rmx, tr, &sc); /* local-only mode. cmdline opts processing has already assured that --local set */
else if (esl_opt_GetBoolean(go, "--msv")) p7_Die("We used to be able to do a generic MSV algorithm - but no longer");
}
/* Optional: get Viterbi alignment length too. */
if (esl_opt_GetBoolean(go, "-a")) /* -a only works with Viterbi; getopts has checked this already; <tr> must be valid */
{
p7_trace_GetStateUseCounts(tr, scounts);
/* there's various ways we could counts "alignment length".
* Here we'll use the total length of model used, in nodes: M+D states.
* score vs al would gives us relative entropy / model position.
*/
/* alilens[i] = scounts[p7T_D] + scounts[p7T_I]; SRE: temporarily testing this instead */
alilens[i] = scounts[p7T_ML] + scounts[p7T_DL] + scounts[p7T_IL] +
scounts[p7T_MG] + scounts[p7T_DG] + scounts[p7T_IG];
p7_trace_Reuse(tr);
}
p7_bg_NullOne(cfg->bg, dsq, L, &nullsc);
scores[i] = (sc - nullsc) / eslCONST_LOG2;
if (cx) p7_checkptmx_Reuse(cx);
if (fx) p7_filtermx_Reuse(fx);
p7_refmx_Reuse(rmx);
}
status = eslOK;
/* deliberate flowthru */
ERROR:
if (dsq != NULL) free(dsq);
p7_checkptmx_Destroy(cx);
p7_filtermx_Destroy(fx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_refmx_Destroy(rmx);
p7_trace_Destroy(tr);
if (status == eslEMEM) sprintf(errbuf, "allocation failure");
return status;
}
