static int storemaxmatchquery(void *info,
GT_UNUSED const GtEncseq *encseq,
const GtQuerymatch *querymatch,
GT_UNUSED const GtUchar *query,
GT_UNUSED GtUword query_totallength,
GT_UNUSED GtError *err)
{
GtArray *tab = (GtArray *) info;
Substringmatch subm;
subm.len = gt_querymatch_querylen(querymatch);
subm.dbstart = gt_querymatch_dbstart(querymatch);
subm.querystart = gt_querymatch_querystart(querymatch);
subm.queryseqnum = gt_querymatch_queryseqnum(querymatch);
gt_array_add(tab,subm);
return 0;
}
static int gt_processxdropquerymatches(void *info,
const GtEncseq *encseq,
const GtQuerymatch *querymatch,
const GtUchar *query,
GtUword query_totallength,
GtError *err)
{
GtXdropmatchinfo *xdropmatchinfo = (GtXdropmatchinfo *) info;
GtXdropscore score;
GtUword querystart, dblen, dbstart, querylen;
GtUword pos1 = gt_querymatch_dbstart(querymatch);
GtUword pos2 = gt_querymatch_querystart(querymatch);
GtUword len = gt_querymatch_querylen(querymatch);
const GtUword dbtotallength = gt_encseq_total_length(encseq);
uint64_t queryseqnum;
GtUword dbseqnum, dbseqstartpos, dbseqlength;
dbseqnum = gt_encseq_seqnum(encseq,pos1);
dbseqstartpos = gt_encseq_seqstartpos(encseq,dbseqnum);
dbseqlength = gt_encseq_seqlength(encseq,dbseqnum);
if (pos1 > 0 && pos2 > 0)
{
gt_assert(dbseqstartpos < pos1);
gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,encseq,
pos1 - dbseqstartpos,0);
gt_seqabstract_reinit_gtuchar(xdropmatchinfo->vseq, query, pos2, 0);
gt_evalxdroparbitscoresextend(false,
&xdropmatchinfo->best_left,
xdropmatchinfo->res,
xdropmatchinfo->useq,
xdropmatchinfo->vseq,
pos1,
pos2,
xdropmatchinfo->belowscore);
} else
{
xdropmatchinfo->best_left.ivalue = 0;
xdropmatchinfo->best_left.jvalue = 0;
xdropmatchinfo->best_left.score = 0;
}
if (pos1 + len < dbtotallength && pos2 + len < query_totallength)
{
gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,
encseq,dbseqstartpos + dbseqlength -
(pos1 + len),0);
gt_seqabstract_reinit_gtuchar(xdropmatchinfo->vseq,
query,query_totallength - (pos2 + len), 0);
gt_evalxdroparbitscoresextend(true,
&xdropmatchinfo->best_right,
xdropmatchinfo->res,
xdropmatchinfo->useq,
xdropmatchinfo->vseq,
pos1 + len,
pos2 + len,
xdropmatchinfo->belowscore);
} else
{
xdropmatchinfo->best_right.ivalue = 0;
xdropmatchinfo->best_right.jvalue = 0;
xdropmatchinfo->best_right.score = 0;
}
gt_assert(pos1 >= (GtUword) xdropmatchinfo->best_left.ivalue &&
pos2 >= (GtUword) xdropmatchinfo->best_left.jvalue);
querystart = pos2 - xdropmatchinfo->best_left.jvalue;
queryseqnum = gt_querymatch_queryseqnum(querymatch);
dblen = len + xdropmatchinfo->best_left.ivalue
+ xdropmatchinfo->best_right.ivalue;
dbstart = pos1 - xdropmatchinfo->best_left.ivalue;
querylen = len + xdropmatchinfo->best_left.jvalue
+ xdropmatchinfo->best_right.jvalue,
score = (GtXdropscore) len * xdropmatchinfo->arbitscores.mat +
xdropmatchinfo->best_left.score +
xdropmatchinfo->best_right.score;
gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,
encseq,
dblen,
dbstart);
gt_seqabstract_reinit_gtuchar(xdropmatchinfo->vseq, query, querylen,
querystart);
gt_querymatch_fill(xdropmatchinfo->querymatchspaceptr,
dblen,
dbstart,
GT_READMODE_FORWARD,
false,
score,
greedyunitedist(xdropmatchinfo->frontresource,
xdropmatchinfo->useq,xdropmatchinfo->vseq),
false,
queryseqnum,
querylen,
querystart);
return gt_querymatch_output(info, encseq, xdropmatchinfo->querymatchspaceptr,
query, query_totallength,
err);
}
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);
}
}
