static int
rejustify_insertions_text(const ESL_ALPHABET *abc, ESL_MSA *msa, const int *inserts, const int *matmap, const int *matuse, int M)
{
int idx;
int k;
int apos;
int nins;
int npos, opos;
for (idx = 0; idx < msa->nseq; idx++)
{
for (k = 0; k < M; k++)
if (inserts[k] > 1)
{
for (nins = 0, apos = matmap[k]; apos < matmap[k+1]-matuse[k+1]; apos++)
if (esl_abc_CIsResidue(abc, msa->aseq[idx][apos])) nins++;
if (k == 0) nins = 0; /* N-terminus is right justified */
else nins /= 2; /* split in half; nins now = # of residues left left-justified */
opos = npos = -1+matmap[k+1]-matuse[k+1];
while (opos >= matmap[k]+nins) {
if (esl_abc_CIsGap(abc, msa->aseq[idx][opos])) opos--;
else {
msa->aseq[idx][npos] = msa->aseq[idx][opos];
if (msa->pp != NULL && msa->pp[idx] != NULL) msa->pp[idx][npos] = msa->pp[idx][opos];
npos--;
opos--;
}
}
while (npos >= matmap[k]+nins) {
msa->aseq[idx][npos] = '.';
if (msa->pp != NULL && msa->pp[idx] != NULL) msa->pp[idx][npos] = '.';
npos--;
}
}
}
return eslOK;
}
/* Function: p7_alidisplay_Backconvert()
* Synopsis: Convert an alidisplay to a faux trace and subsequence.
* Incept: SRE, Wed Dec 10 09:49:28 2008 [Janelia]
*
* Purpose: Convert alignment display object <ad> to a faux subsequence
* and faux subsequence trace, returning them in <ret_sq> and
* <ret_tr>.
*
* The subsequence <*ret_sq> is digital; ascii residues in
* <ad> are digitized using digital alphabet <abc>.
*
* The subsequence and trace are suitable for passing as
* array elements to <p7_MultipleAlignment>. This is the
* main purpose of backconversion. Results of a profile
* search are stored in a hit list as a processed
* <P7_ALIDISPLAY>, not as a <P7_TRACE> and <ESL_SQ>, to
* reduce space and to reduce communication overhead in
* parallelized search implementations. After reduction
* to a final hit list, a master may want to construct a
* multiple alignment of all the significant hits.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> on allocation failures. <eslECORRUPT> on unexpected internal
* data corruption. On any exception, <*ret_sq> and <*ret_tr> are
* <NULL>.
*
* Xref: J4/29.
*/
int
p7_alidisplay_Backconvert(const P7_ALIDISPLAY *ad, const ESL_ALPHABET *abc, ESL_SQ **ret_sq, P7_TRACE **ret_tr)
{
ESL_SQ *sq = NULL; /* RETURN: faux subsequence */
P7_TRACE *tr = NULL; /* RETURN: faux trace */
int subL = 0; /* subsequence length in the <ad> */
int a, i, k; /* coords for <ad>, <sq->dsq>, model */
char st; /* state type: MDI */
int status;
/* Make a first pass over <ad> just to calculate subseq length */
for (a = 0; a < ad->N; a++)
if (! esl_abc_CIsGap(abc, ad->aseq[a])) subL++;
/* Allocations */
if ((sq = esl_sq_CreateDigital(abc)) == NULL) { status = eslEMEM; goto ERROR; }
if ((status = esl_sq_GrowTo(sq, subL)) != eslOK) goto ERROR;
if ((tr = (ad->ppline == NULL) ? p7_trace_Create() : p7_trace_CreateWithPP()) == NULL) { status = eslEMEM; goto ERROR; }
if ((status = p7_trace_GrowTo(tr, subL+6)) != eslOK) goto ERROR; /* +6 is for SNB/ECT */
/* Construction of dsq, trace */
sq->dsq[0] = eslDSQ_SENTINEL;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_S, 0, 0) : p7_trace_AppendWithPP(tr, p7T_S, 0, 0, 0.0))) != eslOK) goto ERROR;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_N, 0, 0) : p7_trace_AppendWithPP(tr, p7T_N, 0, 0, 0.0))) != eslOK) goto ERROR;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_B, 0, 0) : p7_trace_AppendWithPP(tr, p7T_B, 0, 0, 0.0))) != eslOK) goto ERROR;
k = ad->hmmfrom;
i = 1;
for (a = 0; a < ad->N; a++)
{
if (esl_abc_CIsResidue(abc, ad->model[a])) { st = (esl_abc_CIsResidue(abc, ad->aseq[a]) ? p7T_M : p7T_D); } else st = p7T_I;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, st, k, i) : p7_trace_AppendWithPP(tr, st, k, i, p7_alidisplay_DecodePostProb(ad->ppline[a])))) != eslOK) goto ERROR;
switch (st) {
case p7T_M: sq->dsq[i] = esl_abc_DigitizeSymbol(abc, ad->aseq[a]); k++; i++; break;
case p7T_I: sq->dsq[i] = esl_abc_DigitizeSymbol(abc, ad->aseq[a]); i++; break;
case p7T_D: k++; break;
}
}
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_E, 0, 0) : p7_trace_AppendWithPP(tr, p7T_E, 0, 0, 0.0))) != eslOK) goto ERROR;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_C, 0, 0) : p7_trace_AppendWithPP(tr, p7T_C, 0, 0, 0.0))) != eslOK) goto ERROR;
if ((status = ((ad->ppline == NULL) ? p7_trace_Append(tr, p7T_T, 0, 0) : p7_trace_AppendWithPP(tr, p7T_T, 0, 0, 0.0))) != eslOK) goto ERROR;
sq->dsq[i] = eslDSQ_SENTINEL;
/* some sanity checks */
if (tr->N != ad->N + 6) ESL_XEXCEPTION(eslECORRUPT, "backconverted trace ended up with unexpected size (%s/%s)", ad->sqname, ad->hmmname);
if (k != ad->hmmto + 1) ESL_XEXCEPTION(eslECORRUPT, "backconverted trace didn't end at expected place on model (%s/%s)", ad->sqname, ad->hmmname);
if (i != subL + 1) ESL_XEXCEPTION(eslECORRUPT, "backconverted subseq didn't end at expected length (%s/%s)", ad->sqname, ad->hmmname);
/* Set up <sq> annotation as a subseq of a source sequence */
if ((status = esl_sq_FormatName(sq, "%s/%ld-%ld", ad->sqname, ad->sqfrom, ad->sqto)) != eslOK) goto ERROR;
if ((status = esl_sq_FormatDesc(sq, "[subseq from] %s", ad->sqdesc[0] != '\0' ? ad->sqdesc : ad->sqname)) != eslOK) goto ERROR;
if ((status = esl_sq_SetSource (sq, ad->sqname)) != eslOK) goto ERROR;
if (ad->sqacc[0] != '\0') { if ((status = esl_sq_SetAccession (sq, ad->sqacc)) != eslOK) goto ERROR; }
sq->n = subL;
sq->start = ad->sqfrom;
sq->end = ad->sqto;
sq->C = 0;
sq->W = subL;
sq->L = ad->L;
tr->M = ad->M;
tr->L = ad->L;
*ret_sq = sq;
*ret_tr = tr;
return eslOK;
ERROR:
if (sq != NULL) esl_sq_Destroy(sq);
if (tr != NULL) p7_trace_Destroy(tr);
*ret_sq = NULL;
*ret_tr = NULL;
return status;
}