/* create an local alignment in square space with constant score values,
* to use it in linear context you have to generate an spacemanager before,
* in any other case it can be NULL */
GtWord alignment_in_square_space_local(GtLinspaceManagement *spacemanager,
GtAlignment *align,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen,
GtWord matchscore,
GtWord mismatchscore,
GtWord gapscore)
{
GtWord score;
gt_assert(align);
GtScoreHandler *scorehandler = gt_scorehandler_new(matchscore,
mismatchscore, 0,
gapscore);
score = alignment_in_square_space_local_generic(spacemanager, align,
useq, ustart, ulen,
vseq, vstart, vlen,
scorehandler);
gt_scorehandler_delete(scorehandler);
return score;
}
/* determining start and end of local alignment and call global function */
GtWord gt_computelinearspace_local_generic(LinspaceManagement *spacemanager,
GtScoreHandler *scorehandler,
GtAlignment *align,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen)
{
GtWord *Ltabcolumn, GT_UNUSED score = GT_WORD_MAX;
GtUwordPair *Starttabcolumn;
GtUword ulen_part, ustart_part, vlen_part, vstart_part;
Gtmaxcoordvalue *max;
gt_assert(spacemanager && scorehandler && align);
gt_linspaceManagement_set_ulen(spacemanager,ulen);
if (ulen == 0UL || vlen == 0UL)
{
/* empty alignment */
return 0;
}
else if (vlen == 1UL)
{
gt_linspaceManagement_check_local(spacemanager,
(ulen+1)*(vlen+1)-1, ulen,
sizeof (GtWord),
sizeof (GtWord *));
return alignment_in_square_space_local_generic(spacemanager, align,
useq, ustart, ulen,
vseq, vstart, vlen,
scorehandler);
}
else if (gt_linspaceManagement_checksquare_local(spacemanager, ulen, vlen,
sizeof (*Ltabcolumn),
sizeof (*Starttabcolumn)))
{
/* call 2dim */
return alignment_in_square_space_local_generic(spacemanager, align,
useq, ustart, ulen,
vseq, vstart, vlen,
scorehandler);
}
gt_linspaceManagement_check_local(spacemanager,
ulen, vlen,
sizeof (*Ltabcolumn),
sizeof (*Starttabcolumn));
max = evaluateallLScolumns(spacemanager, scorehandler,
useq, ustart, ulen,
vseq, vstart, vlen);
if (gt_max_get_length_safe(max))
{
ustart_part = ustart+(gt_max_get_start(max)).a;
vstart_part = vstart+(gt_max_get_start(max)).b;
ulen_part = gt_max_get_row_length(max);
vlen_part = gt_max_get_col_length(max);
score = gt_max_get_value(max);
gt_scorehandler_change_score_to_cost(scorehandler);
gt_alignment_set_seqs(align, &useq[ustart_part], ulen_part,
&vseq[vstart_part], vlen_part);
/* call global function */
gt_calc_linearalign(spacemanager,
gt_scorehandler_get_costhandler(scorehandler), align,
useq, ustart_part, ulen_part,
vseq, vstart_part, vlen_part);
} else
{
/*empty alignment */
return 0;
}
return score;
}
