int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
ESL_STOPWATCH *w = esl_stopwatch_Create();
ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_GMX *gx1 = NULL;
P7_GMX *gx2 = NULL;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
float null2[p7_MAXCODE];
int i;
float fsc, bsc;
double Mcs;
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, L);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
gx1 = p7_gmx_Create(gm->M, L);
gx2 = p7_gmx_Create(gm->M, L);
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_GForward (dsq, L, gm, gx1, &fsc);
p7_GBackward(dsq, L, gm, gx2, &bsc);
p7_GDecoding(gm, gx1, gx2, gx2);
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
p7_GNull2_ByExpectation(gm, gx2, null2);
esl_stopwatch_Stop(w);
Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / w->user;
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("# M = %d\n", gm->M);
printf("# %.1f Mc/s\n", Mcs);
free(dsq);
p7_gmx_Destroy(gx1);
p7_gmx_Destroy(gx2);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
esl_stopwatch_Destroy(w);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return 0;
}
/* compare results to GDecoding(). */
static void
utest_null2_expectation(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N, float tolerance)
{
char *msg = "decoding unit test failed";
P7_HMM *hmm = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
P7_OMX *fwd = p7_omx_Create(M, L, L);
P7_OMX *bck = p7_omx_Create(M, L, L);
P7_OMX *pp = p7_omx_Create(M, L, L);
P7_GMX *gxf = p7_gmx_Create(M, L);
P7_GMX *gxb = p7_gmx_Create(M, L);
P7_GMX *gpp = p7_gmx_Create(M, L);
float *on2 = malloc(sizeof(float) * abc->Kp);
float *gn2 = malloc(sizeof(float) * abc->Kp);
float fsc1, fsc2;
float bsc1, bsc2;
if (!gn2 || !on2) esl_fatal(msg);
if (p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om) != eslOK) esl_fatal(msg);
while (N--)
{
if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal(msg);
if (p7_Forward (dsq, L, om, fwd, &fsc1) != eslOK) esl_fatal(msg);
if (p7_Backward (dsq, L, om, fwd, bck, &bsc1) != eslOK) esl_fatal(msg);
if (p7_Decoding(om, fwd, bck, pp) != eslOK) esl_fatal(msg);
if (p7_Null2_ByExpectation(om, pp, on2) != eslOK) esl_fatal(msg);
if (p7_GForward (dsq, L, gm, gxf, &fsc2) != eslOK) esl_fatal(msg);
if (p7_GBackward(dsq, L, gm, gxb, &bsc2) != eslOK) esl_fatal(msg);
if (p7_GDecoding(gm, gxf, gxb, gpp) != eslOK) esl_fatal(msg);
if (p7_GNull2_ByExpectation(gm, gpp, gn2) != eslOK) esl_fatal(msg);
if (esl_vec_FCompare(gn2, on2, abc->Kp, tolerance) != eslOK) esl_fatal(msg);
}
p7_gmx_Destroy(gpp);
p7_gmx_Destroy(gxf);
p7_gmx_Destroy(gxb);
p7_omx_Destroy(pp);
p7_omx_Destroy(fwd);
p7_omx_Destroy(bck);
free(on2);
free(gn2);
free(dsq);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_hmm_Destroy(hmm);
}
/* glocal_rescore_isolated_domain()
* EPN, Tue Oct 5 10:16:12 2010
*
* Based on p7_domaindef.c's rescore_isolated_domain(). Modified
* so that generic matrices (which can be used for glocally configured
* models) can be used. This function finds a single glocal domain, not a
* single local one.
*
* Also modified to optionally remove the Backward and OA alignment.
* The decision to do these is determined by three input parameters:
* <null2_is_done>: TRUE if we've already computed the null2 scores for
* this region (see Sean's notes below).
* <do_null2>: TRUE if we will apply a null2 penalty eventually
* to this domain
* <do_aln>: TRUE if we need the OA alignment
*
* Notes (verbatim) from p7_domaindef.c::rescore_isolated_domain():
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* SRE, Fri Feb 8 09:18:33 2008 [Janelia]
*
* We have isolated a single domain's envelope from <i>..<j> in
* sequence <sq>, and now we want to score it in isolation and obtain
* an alignment display for it.
*
* (Later, we can add up all the individual domain scores from this
* seq into a new per-seq score, to compare to the original per-seq
* score).
*
* The caller provides model <om> configured in unilocal mode; by
* using unilocal (as opposed to multilocal), we're going to force the
* identification of a single domain in this envelope now.
*
* The alignment is an optimal accuracy alignment (sensu IH Holmes),
* also obtained in unilocal mode.
*
* The caller provides DP matrices <ox1> and <ox2> with sufficient
* space to hold Forward and Backward calculations for this domain
* against the model. (The caller will typically already have matrices
* sufficient for the complete sequence lying around, and can just use
* those.) The caller also provides a <P7_DOMAINDEF> object which is
* (efficiently, we trust) managing any necessary temporary working
* space and heuristic thresholds.
*
* Returns <eslOK> if a domain was successfully identified, scored,
* and aligned in the envelope; if so, the per-domain information is
* registered in <ddef>, in <ddef->dcl>.
*
* And here's what's happened to our working memory:
*
* <ddef>: <ddef->tr> has been used, and possibly reallocated, for
* the OA trace of the domain. Before exit, we called
* <Reuse()> on it.
*
* <ox1> : happens to be holding OA score matrix for the domain
* upon return, but that's not part of the spec; officially
* its contents are "undefined".
*
* <ox2> : happens to be holding a posterior probability matrix
* for the domain upon return, but we're not making that
* part of the spec, so caller shouldn't rely on this;
* spec just makes its contents "undefined".
*/
static int
glocal_rescore_isolated_domain(P7_DOMAINDEF *ddef, const P7_PROFILE *gm, const ESL_SQ *sq,
P7_GMX *gx1, P7_GMX *gx2, int i, int j, int null2_is_done,
int do_null2, int do_aln)
{
P7_DOMAIN *dom = NULL;
int Ld = j-i+1;
float domcorrection = 0.0;
float envsc, oasc;
int z;
int pos;
float null2[p7_MAXCODE];
int status;
p7_GForward (sq->dsq + i-1, Ld, gm, gx1, &envsc);
oasc = 0.;
if(do_null2 || do_aln) {
p7_GBackward(sq->dsq + i-1, Ld, gm, gx2, NULL);
status = p7_GDecoding(gm, gx1, gx2, gx2); /* <ox2> is now overwritten with post probabilities */
if (status == eslERANGE) return eslFAIL; /* rare: numeric overflow; domain is assumed to be repetitive garbage [J3/119-212] */
/* Is null2 set already for this i..j? (It is, if we're in a domain that
* was defined by stochastic traceback clustering in a multidomain region;
* it isn't yet, if we're in a simple one-domain region). If it isn't,
* do it now, by the expectation (posterior decoding) method.
*/
if ((! null2_is_done) && do_null2) {
p7_GNull2_ByExpectation(gm, gx2, null2);
for (pos = i; pos <= j; pos++)
ddef->n2sc[pos] = logf(null2[sq->dsq[pos]]);
}
if(do_null2) {
for (pos = i; pos <= j; pos++)
domcorrection += ddef->n2sc[pos]; /* domcorrection is in units of NATS */
}
if(do_aln) {
/* Find an optimal accuracy alignment */
p7_GOptimalAccuracy(gm, gx2, gx1, &oasc); /* <ox1> is now overwritten with OA scores */
p7_GOATrace (gm, gx2, gx1, ddef->tr); /* <tr>'s seq coords are offset by i-1, rel to orig dsq */
/* hack the trace's sq coords to be correct w.r.t. original dsq */
for (z = 0; z < ddef->tr->N; z++)
if (ddef->tr->i[z] > 0) ddef->tr->i[z] += i-1;
}
/* get ptr to next empty domain structure in domaindef's results */
}
if (ddef->ndom == ddef->nalloc) {
void *p;
ESL_RALLOC(ddef->dcl, p, sizeof(P7_DOMAIN) * (ddef->nalloc*2));
ddef->nalloc *= 2;
}
dom = &(ddef->dcl[ddef->ndom]);
/* store the results in it */
dom->ienv = i;
dom->jenv = j;
dom->envsc = envsc; /* in units of NATS */
dom->domcorrection = domcorrection; /* in units of NATS, will be 0. if do_null2 == FALSE */
dom->oasc = oasc; /* in units of expected # of correctly aligned residues, will be 0. if do_aln == FALSE */
dom->dombias = 0.0; /* gets set later, using bg->omega and dombias */
dom->bitscore = 0.0; /* gets set later by caller, using envsc, null score, and dombias */
dom->lnP = 1.0; /* gets set later by caller, using bitscore */
dom->is_reported = FALSE; /* gets set later by caller */
dom->is_included = FALSE; /* gets set later by caller */
dom->ad = NULL;
dom->iali = i;
dom->jali = j;
ddef->ndom++;
if(do_aln) {
p7_trace_Reuse(ddef->tr);
}
return eslOK;
ERROR:
if(do_aln) {
p7_trace_Reuse(ddef->tr);
}
return status;
}
