static int gt_simpleexactselfmatchoutput(void *info,
const GtEncseq *encseq,
unsigned long len,
unsigned long pos1,
unsigned long pos2,
GT_UNUSED GtError *err)
{
unsigned long queryseqnum, seqstartpos, seqlength;
GtQuerymatch *querymatch = (GtQuerymatch *) info;
if (pos1 > pos2)
{
unsigned long tmp = pos1;
pos1 = pos2;
pos2 = tmp;
}
queryseqnum = gt_encseq_seqnum(encseq,pos2);
seqstartpos = gt_encseq_seqstartpos(encseq, queryseqnum);
seqlength = gt_encseq_seqlength(encseq, queryseqnum);
gt_assert(pos2 >= seqstartpos);
gt_querymatch_fill(querymatch,
len,
pos1,
GT_READMODE_FORWARD,
false,
0,
0,
true,
(uint64_t) queryseqnum,
len,
pos2 - seqstartpos);
return gt_querymatch_output(info, encseq, querymatch, NULL, seqlength, err);
}
int gt_querymatch_fill_and_output(
GtUword dblen,
GtUword dbstart,
GtReadmode readmode,
bool query_as_reversecopy,
GtWord score,
GtUword edist,
bool selfmatch,
uint64_t queryseqnum,
GtUword querylen,
GtUword querystart,
GtQuerymatchoutoptions *querymatchoutoptions,
const GtEncseq *encseq,
const GtUchar *query,
GtUword query_totallength,
GtError *err)
{
GtQuerymatch querymatch;
gt_querymatch_fill(&querymatch,
dblen,
dbstart,
readmode,
query_as_reversecopy,
score,
edist,
selfmatch,
queryseqnum,
querylen,
querystart);
return gt_querymatch_output(querymatchoutoptions,
encseq,
&querymatch,
query,
query_totallength,
err);
}
static int gt_simpleexactselfmatchoutput(void *info,
const GtGenericEncseq *genericencseq,
GtUword len,
GtUword pos1,
GtUword pos2,
GT_UNUSED GtError *err)
{
GtUword queryseqnum, seqstartpos, seqlength;
GtQuerymatch *querymatch = (GtQuerymatch *) info;
const GtEncseq *encseq;
if (pos1 > pos2)
{
GtUword tmp = pos1;
pos1 = pos2;
pos2 = tmp;
}
gt_assert(genericencseq != NULL && genericencseq->hasencseq);
encseq = genericencseq->seqptr.encseq;
queryseqnum = gt_encseq_seqnum(encseq,pos2);
seqstartpos = gt_encseq_seqstartpos(encseq, queryseqnum);
seqlength = gt_encseq_seqlength(encseq, queryseqnum);
gt_assert(pos2 >= seqstartpos);
gt_querymatch_fill(querymatch,
len,
pos1,
GT_READMODE_FORWARD,
false,
0,
0,
true,
(uint64_t) queryseqnum,
len,
pos2 - seqstartpos);
return gt_querymatch_output(info, encseq, querymatch, NULL, seqlength, 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);
}
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);
}
