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 int gt_simplexdropselfmatchoutput(void *info,
const GtGenericEncseq *genericencseq,
GtUword len,
GtUword pos1,
GtUword pos2,
GtError *err)
{
GtXdropmatchinfo *xdropmatchinfo = (GtXdropmatchinfo *) info;
GtXdropscore score;
GtUword dbseqnum, dbseqstartpos, dbseqlength, dbstart, dblen,
querystart, queryseqnum, querylen, queryseqlength,
queryseqstartpos, dbtotallength;
const GtEncseq *encseq;
gt_assert(genericencseq != NULL && genericencseq->hasencseq);
encseq = genericencseq->seqptr.encseq;
dbtotallength = gt_encseq_total_length(encseq);
if (pos1 > pos2)
{
GtUword tmp = pos1;
pos1 = pos2;
pos2 = tmp;
}
dbseqnum = gt_encseq_seqnum(encseq,pos1),
dbseqstartpos = gt_encseq_seqstartpos(encseq,dbseqnum),
dbseqlength = gt_encseq_seqlength(encseq,dbseqnum);
if (pos2 < dbseqstartpos + dbseqlength)
{
queryseqnum = dbseqnum;
queryseqstartpos = dbseqstartpos;
queryseqlength = dbseqlength;
} else
{
queryseqnum = gt_encseq_seqnum(encseq,pos2);
gt_assert(dbseqnum < queryseqnum);
queryseqstartpos = gt_encseq_seqstartpos(encseq,queryseqnum);
queryseqlength = gt_encseq_seqlength(encseq,queryseqnum);
}
if (pos1 > 0 && pos2 > 0)
{
gt_assert(pos1 >= dbseqstartpos && pos2 >= queryseqstartpos);
gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,encseq,
pos1 - dbseqstartpos,0);
gt_seqabstract_reinit_encseq(xdropmatchinfo->vseq,encseq,
pos2 - queryseqstartpos,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 < dbtotallength)
{
const GtUword seqend1 = dbseqstartpos + dbseqlength;
const GtUword seqend2 = queryseqstartpos + queryseqlength;
gt_assert(seqend1 >= pos1 + len && seqend2 >= pos2 + len);
gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,
encseq,seqend1 - (pos1 + len),0);
gt_seqabstract_reinit_encseq(xdropmatchinfo->vseq,
encseq,seqend2 - (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;
gt_assert(querystart >= queryseqstartpos);
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_encseq(xdropmatchinfo->vseq,
encseq,
querylen,
querystart);
gt_querymatch_fill(xdropmatchinfo->querymatchspaceptr,
dblen,
dbstart,
GT_READMODE_FORWARD,
false,
score,
greedyunitedist(xdropmatchinfo->frontresource,
xdropmatchinfo->useq,xdropmatchinfo->vseq),
true,
(uint64_t) queryseqnum,
querylen,
querystart - queryseqstartpos);
return gt_querymatch_output(info, encseq, xdropmatchinfo->querymatchspaceptr,
NULL, gt_encseq_seqlength(encseq, queryseqnum),
err);
}
int gt_xdrop_unit_test(GT_UNUSED GtError *err)
{
int had_err = 0, i, j, s;
const GtUchar *strings[GT_XDROP_NUM_OF_TESTS] =
{(const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCCAAAGGGTTTCCCTTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTTTTTGGGGCCCCAAAATTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTNNNNTTTTGGGGCCCCAAAATTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCGCAAAGGGTTTCCCTTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCAAAGGGTTTCCCCTTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCTCAAAGGGTTTCCTTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTAAACAGATCACCCGCTTTTTTTTTTTTTTTT",
(const GtUchar*) "TTTTTTTTTTTTTTTAAACGGGTTTCTCAAAGGGTTCCCTTTTTTTTTTTTTTT"};
GtUword lengths[GT_XDROP_NUM_OF_TESTS] =
{54UL, 46UL, 50UL, 54UL, 54UL, 54UL, 46UL, 54UL},
eval_scores[GT_XDROP_NUM_OF_TESTS *
GT_XDROP_NUM_OF_TESTS *
GT_XDROP_NUM_OF_TESTS] =
{0, 13UL, 0, 1UL, 4UL, 1UL, 0, 7UL,
13UL, 0, 0, 14UL, 15UL, 14UL, 0, 15UL,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 14UL, 0, 0, 1UL, 2UL, 0, 1UL,
4UL, 15UL, 0, 1UL, 0, 8UL, 0, 1UL,
1UL, 14UL, 0, 2UL, 8UL, 0, 0, 4UL,
0, 0, 0, 0, 0, 0, 0, 0,
7UL, 15UL, 0, 1UL, 1UL, 4UL, 0, 0,
0, 13UL, 0, 1UL, 4UL, 5UL, 14UL, 7UL,
13UL, 0, 0, 14UL, 15UL, 14UL, 12UL, 15UL,
0, 0, 0, 20UL, 0, 19UL, 17UL, 0,
1UL, 14UL, 20UL, 0, 5UL, 6UL, 15UL, 8UL,
4UL, 15UL, 0, 5UL, 0, 8UL, 15UL, 10UL,
5UL, 14UL, 19UL, 6UL, 8UL, 0, 14UL, 4UL,
14UL, 12UL, 17UL, 15UL, 15UL, 14UL, 0, 14UL,
7UL, 15UL, 0, 8UL, 10UL, 4UL, 14UL, 0,
0, 13UL, 19UL, 1UL, 2UL, 2UL, 13UL, 3UL,
13UL, 0, 9UL, 14UL, 14UL, 13UL, 12UL, 14UL,
17UL, 4UL, 0, 18UL, 19UL, 16UL, 16UL, 18UL,
1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL,
2UL, 14UL, 18UL, 2UL, 0, 4UL, 13UL, 4UL,
2UL, 13UL, 19UL, 3UL, 4UL, 0, 13UL, 3UL,
14UL, 12UL, 17UL, 13UL, 13UL, 14UL, 0, 14UL,
3UL, 14UL, 18UL, 3UL, 4UL, 3UL, 13UL, 0,
0, 13UL, 17UL, 1UL, 2UL, 2UL, 14UL, 3UL,
13UL, 0, 4UL, 14UL, 15UL, 13UL, 12UL, 14UL,
19UL, 9UL, 0, 18UL, 18UL, 19UL, 17UL, 18UL,
1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL,
2UL, 14UL, 19UL, 2UL, 0, 4UL, 13UL, 4UL,
2UL, 13UL, 16UL, 3UL, 4UL, 0, 14UL, 3UL,
13UL, 12UL, 16UL, 13UL, 13UL, 13UL, 0, 13UL,
3UL, 14UL, 18UL, 3UL, 4UL, 3UL, 14UL, 0,
0, 0, 0, 1UL, 1UL, 1UL, 0, 1UL,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 0, 0, 0, 1UL, 0, 0, 1UL,
1UL, 0, 0, 1UL, 0, 0, 0, 1UL,
1UL, 0, 0, 0, 0, 0, 0, 1UL,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 0, 0, 1UL, 1UL, 1UL, 0, 0,
0, 0, 0, 1UL, 1UL, 1UL, 0, 1UL,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 0, 0, 0, 1UL, 2UL, 0, 1UL,
1UL, 0, 0, 1UL, 0, 0, 0, 1UL,
1UL, 0, 0, 2UL, 0, 0, 0, 1UL,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 0, 0, 1UL, 1UL, 1UL, 0, 0,
0, 13UL, 17UL, 1UL, 2UL, 2UL, 13UL, 3UL,
13UL, 0, 4UL, 14UL, 14UL, 13UL, 12UL, 14UL,
17UL, 4UL, 0, 18UL, 19UL, 16UL, 16UL, 19UL,
1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL,
2UL, 14UL, 19UL, 2UL, 0, 4UL, 13UL, 4UL,
2UL, 13UL, 16UL, 3UL, 4UL, 0, 13UL, 3UL,
13UL, 12UL, 16UL, 13UL, 13UL, 13UL, 0, 13UL,
3UL, 14UL, 19UL, 3UL, 4UL, 3UL, 13UL, 0,
0, 13UL, 0, 1UL, 2UL, 2UL, 5UL, 3UL,
13UL, 0, 0, 14UL, 15UL, 13UL, 0, 14UL,
0, 0, 0, 0, 0, 0, 0, 0,
1UL, 14UL, 0, 0, 2UL, 3UL, 5UL, 3UL,
2UL, 15UL, 0, 2UL, 0, 4UL, 5UL, 4UL,
2UL, 13UL, 0, 3UL, 4UL, 0, 6UL, 3UL,
5UL, 0, 0, 5UL, 5UL, 6UL, 0, 5UL,
3UL, 14UL, 0, 3UL, 4UL, 3UL, 5UL, 0};
GtSeqabstract *useq, *vseq;
GtXdropArbitraryscores score[GT_XDROP_NUM_OF_TESTS] = {{2, -2, -2, -2},
{2, -1, -1, -1},
{2, -1, -5, -2},
{2, -1, -2, -5},
{3, -2, -3, -3},
{3, -1, -1, -1},
{4, -1, -3, -3},
{10, -3, -8, -8}};
GtXdropresources *resources;
GtXdropbest best;
GtXdropscore dropscore = (GtXdropscore) 12;
GtMultieoplist *edit_ops = NULL;
GtAlignment *alignment;
bool rightextension = true;
gt_error_check(err);
for (s = 0; s < GT_XDROP_NUM_OF_TESTS; ++s) {
resources = gt_xdrop_resources_new(&score[s]);
for (i = 0; i < GT_XDROP_NUM_OF_TESTS && !had_err; ++i) {
for (j = 0; j < GT_XDROP_NUM_OF_TESTS; ++j) {
useq = gt_seqabstract_new_gtuchar(rightextension,GT_READMODE_FORWARD,
strings[i], lengths[i], 0,lengths[i]);
vseq = gt_seqabstract_new_gtuchar(rightextension, GT_READMODE_FORWARD,
strings[j], lengths[j], 0,lengths[j]);
gt_evalxdroparbitscoresextend(true, &best, resources, useq, vseq,
dropscore);
edit_ops = gt_xdrop_backtrack(resources, &best);
gt_ensure(edit_ops != NULL);
alignment = gt_alignment_new_with_seqs(strings[i], best.ivalue,
strings[j], best.jvalue);
gt_alignment_set_multieop_list(alignment, edit_ops);
gt_ensure(eval_scores[s*64+i*8+j] == gt_alignment_eval(alignment));
gt_multieoplist_delete(edit_ops);
gt_alignment_delete(alignment);
if (i == j) {
gt_evalxdroparbitscoresextend(false, &best, resources, useq, vseq,
dropscore);
edit_ops = gt_xdrop_backtrack(resources, &best);
alignment = gt_alignment_new_with_seqs(strings[i], best.ivalue,
strings[j], best.jvalue);
gt_alignment_set_multieop_list(alignment, edit_ops);
gt_ensure(eval_scores[s*64+i*8+j] == gt_alignment_eval(alignment));
gt_multieoplist_delete(edit_ops);
gt_alignment_delete(alignment);
}
gt_seqabstract_delete(useq);
gt_seqabstract_delete(vseq);
}
}
gt_xdrop_resources_delete(resources);
}
return had_err;
}
