const void *gt_completealignmentfromLocaliTracebackstate(
GtUword *alignedquerylength,
const Limdfsconstinfo *lci)
{
#ifndef NDEBUG
Scoretype evalscore;
#endif
const GtUchar *querysubstart;
#ifdef SKDEBUG
gt_alignment_show_multieop_list(lci->tbs.alignment,stdout);
#endif
gt_assert(lci->tbs.queryend >= lci->tbs.querypos);
*alignedquerylength = lci->tbs.queryend - lci->tbs.querypos;
querysubstart = lci->query + lci->tbs.querypos;
gt_assert(querysubstart != NULL);
gt_alignment_set_seqs(lci->tbs.alignment,
querysubstart,
*alignedquerylength,
lci->tbs.spaceGtUchardbsubstring,
(GtUword) lci->tbs.dbprefixlen);
#ifndef NDEBUG
evalscore = gt_alignment_eval_with_score(lci->tbs.alignment,false,
lci->scorevalues.matchscore,
lci->scorevalues.mismatchscore,
lci->scorevalues.gapextend);
if (evalscore < 0 || (GtUword) evalscore < lci->threshold)
{
fprintf(stderr,"unexpected eval score "GT_WD"\n",evalscore);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
#endif
return (const void *) lci->tbs.alignment;
}
static void gt_show_seed_extend_plain(GtSequencepairbuffer *seqpairbuf,
GtLinspaceManagement
*linspace_spacemanager,
GtScoreHandler *linspace_scorehandler,
GtAlignment *alignment,
GtUchar *alignment_show_buffer,
GtUword alignmentwidth,
bool showeoplist,
const GtUchar *characters,
GtUchar wildcardshow,
const GtEncseq *aencseq,
const GtEncseq *bencseq,
const GtQuerymatch *querymatchptr)
{
GtUword edist;
GtReadmode query_readmode = gt_querymatch_query_readmode(querymatchptr);
const GtUword distance = gt_querymatch_distance(querymatchptr),
dblen = gt_querymatch_dblen(querymatchptr),
queryseqnum = gt_querymatch_queryseqnum(querymatchptr),
querystart_fwdstrand
= gt_querymatch_querystart_fwdstrand(querymatchptr),
querylen = gt_querymatch_querylen(querymatchptr);
const GtUword apos_ab = gt_querymatch_dbstart(querymatchptr);
const GtUword bpos_ab = gt_encseq_seqstartpos(bencseq, queryseqnum) +
querystart_fwdstrand;
gt_querymatch_coordinates_out(querymatchptr);
if (dblen >= seqpairbuf->a_allocated)
{
seqpairbuf->a_sequence = gt_realloc(seqpairbuf->a_sequence,
sizeof *seqpairbuf->a_sequence * dblen);
seqpairbuf->a_allocated = dblen;
}
if (querylen >= seqpairbuf->b_allocated)
{
seqpairbuf->b_sequence = gt_realloc(seqpairbuf->b_sequence,
sizeof *seqpairbuf->b_sequence *
querylen);
seqpairbuf->b_allocated = querylen;
}
gt_encseq_extract_encoded(aencseq, seqpairbuf->a_sequence, apos_ab,
apos_ab + dblen - 1);
gt_encseq_extract_encoded(bencseq, seqpairbuf->b_sequence, bpos_ab,
bpos_ab + querylen - 1);
if (query_readmode != GT_READMODE_FORWARD)
{
gt_assert(query_readmode == GT_READMODE_REVCOMPL);
gt_inplace_reverse_complement(seqpairbuf->b_sequence,querylen);
}
edist = gt_computelinearspace_generic(linspace_spacemanager,
linspace_scorehandler,
alignment,
seqpairbuf->a_sequence,
0,
dblen,
seqpairbuf->b_sequence,
0,
querylen);
if (edist < distance)
{
printf("# edist=" GT_WU " (smaller by " GT_WU ")\n",edist,distance - edist);
}
gt_assert(edist <= distance);
if (alignmentwidth > 0)
{
gt_alignment_show_generic(alignment_show_buffer,
false,
alignment,
stdout,
alignmentwidth,
characters,
wildcardshow);
}
if (showeoplist && distance > 0)
{
gt_alignment_show_multieop_list(alignment, stdout);
}
if (alignmentwidth > 0 || showeoplist)
{
gt_alignment_reset(alignment);
}
}
