/* annotate()
* Transfer annotation information from MSA to new HMM.
* Also sets model-specific residue composition (hmm->compo).
*/
static int
annotate(P7_BUILDER *bld, const ESL_MSA *msa, P7_HMM *hmm)
{
int status;
/* Name. */
if (msa->name) p7_hmm_SetName(hmm, msa->name);
else ESL_XFAIL(eslEINVAL, bld->errbuf, "Unable to name the HMM.");
if ((status = p7_hmm_SetAccession (hmm, msa->acc)) != eslOK) ESL_XFAIL(status, bld->errbuf, "Failed to record MSA accession");
if ((status = p7_hmm_SetDescription(hmm, msa->desc)) != eslOK) ESL_XFAIL(status, bld->errbuf, "Failed to record MSA description");
// if ((status = p7_hmm_AppendComlog(hmm, go->argc, go->argv)) != eslOK) ESL_XFAIL(status, errbuf, "Failed to record command log");
if ((status = p7_hmm_SetCtime(hmm)) != eslOK) ESL_XFAIL(status, bld->errbuf, "Failed to record timestamp");
if ((status = p7_hmm_SetComposition(hmm)) != eslOK) ESL_XFAIL(status, bld->errbuf, "Failed to determine model composition");
if ((status = p7_hmm_SetConsensus(hmm, NULL)) != eslOK) ESL_XFAIL(status, bld->errbuf, "Failed to set consensus line");
if (msa->cutset[eslMSA_GA1] && msa->cutset[eslMSA_GA2]) { hmm->cutoff[p7_GA1] = msa->cutoff[eslMSA_GA1]; hmm->cutoff[p7_GA2] = msa->cutoff[eslMSA_GA2]; hmm->flags |= p7H_GA; }
if (msa->cutset[eslMSA_TC1] && msa->cutset[eslMSA_TC2]) { hmm->cutoff[p7_TC1] = msa->cutoff[eslMSA_TC1]; hmm->cutoff[p7_TC2] = msa->cutoff[eslMSA_TC2]; hmm->flags |= p7H_TC; }
if (msa->cutset[eslMSA_NC1] && msa->cutset[eslMSA_NC2]) { hmm->cutoff[p7_NC1] = msa->cutoff[eslMSA_NC1]; hmm->cutoff[p7_NC2] = msa->cutoff[eslMSA_NC2]; hmm->flags |= p7H_NC; }
return eslOK;
ERROR:
return status;
}
/* Function: p7_Seqmodel()
* Synopsis: Make a profile HMM from a single sequence.
*
* Purpose: Make a profile HMM from a single sequence, for
* probabilistic Smith/Waterman alignment, HMMER3-style.
*
* The query is digital sequence <dsq> of length <M>
* residues in alphabet <abc>, named <name>.
*
* The scoring system is given by <Q>, <f>, <popen>, and
* <pextend>. <Q> is a $K \times K$ matrix giving
* conditional residue probabilities $P(a \mid b)}$; these
* are typically obtained by reverse engineering a score
* matrix like BLOSUM62. <f> is a vector of $K$ background
* frequencies $p_a$. <popen> and <pextend> are the
* probabilities assigned to gap-open ($t_{MI}$ and
* $t_{MD}$) and gap-extend ($t_{II}$ and $t_{DD}$)
* transitions.
*
* The <p7H_SINGLE> flag is set on the <hmm>. Model
* configuration (<p7_profile_Config(), friends> detects
* this flag. <B->Mk> entry transitions include a match
* state occupancy term for profile HMMs, but for single
* queries, that <occ[]> term is assumed 1.0 for all
* positions. See commentary in modelconfig.c.
*
* Args:
*
* Returns: <eslOK> on success, and a newly allocated HMM is returned
* in <ret_hmm>.
*
* Throws: <eslEMEM> on allocation error, and <*ret_hmm> is <NULL>.
*/
int
p7_Seqmodel(const ESL_ALPHABET *abc, ESL_DSQ *dsq, int M, char *name,
ESL_DMATRIX *Q, float *f, double popen, double pextend,
P7_HMM **ret_hmm)
{
int status;
P7_HMM *hmm = NULL;
char *logmsg = "[HMM created from a query sequence]";
int k;
if ((hmm = p7_hmm_Create(M, abc)) == NULL) { status = eslEMEM; goto ERROR; }
for (k = 0; k <= M; k++)
{
/* Use rows of P matrix as source of match emission vectors */
if (k > 0) esl_vec_D2F(Q->mx[(int) dsq[k]], abc->K, hmm->mat[k]);
/* Set inserts to background for now. This will be improved. */
esl_vec_FCopy(f, abc->K, hmm->ins[k]);
hmm->t[k][p7H_MM] = 1.0 - 2 * popen;
hmm->t[k][p7H_MI] = popen;
hmm->t[k][p7H_MD] = popen;
hmm->t[k][p7H_IM] = 1.0 - pextend;
hmm->t[k][p7H_II] = pextend;
hmm->t[k][p7H_DM] = 1.0 - pextend;
hmm->t[k][p7H_DD] = pextend;
}
/* Deal w/ special stuff at node M, overwriting a little of what we
* just did.
*/
hmm->t[M][p7H_MM] = 1.0 - popen;
hmm->t[M][p7H_MD] = 0.;
hmm->t[M][p7H_DM] = 1.0;
hmm->t[M][p7H_DD] = 0.;
/* Add mandatory annotation
*/
p7_hmm_SetName(hmm, name);
p7_hmm_AppendComlog(hmm, 1, &logmsg);
hmm->nseq = 1;
p7_hmm_SetCtime(hmm);
hmm->checksum = 0;
hmm->flags |= p7H_SINGLE;
*ret_hmm = hmm;
return eslOK;
ERROR:
if (hmm != NULL) p7_hmm_Destroy(hmm);
*ret_hmm = NULL;
return status;
}
