/* global alignment with linear gapcosts in linear space
* with constant cost values */
GtUword gt_computelinearspace(LinspaceManagement *spacemanager,
GtAlignment *align,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen,
GtUword matchcost,
GtUword mismatchcost,
GtUword gapcost)
{
GtUword distance;
GtScoreHandler *scorehandler;
gt_assert(spacemanager && align);
scorehandler = gt_scorehandler_new_DNA(matchcost, mismatchcost, 0, gapcost);
distance = gt_computelinearspace_generic(spacemanager, scorehandler, align,
useq, ustart, ulen,
vseq, vstart, vlen);
gt_scorehandler_delete(scorehandler);
return distance;
}
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);
}
}
