/* create a global alignment in square space with constant cost values,
* to use it in linear context you have to generate an spacemanager before,
* in any other case it can be NULL */
GtUword alignment_in_square_space(GtLinspaceManagement *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(align);
scorehandler = gt_scorehandler_new(matchcost, mismatchcost, 0, gapcost);
distance = alignment_in_square_space_generic (spacemanager, align,
useq, ustart, ulen,
vseq, vstart, vlen,
scorehandler);
gt_scorehandler_delete(scorehandler);
return distance;
}
/* calculating alignment in linear space */
GtUword gt_calc_linearalign(LinspaceManagement *spacemanager,
GtScoreHandler *scorehandler,
GtAlignment *align,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen)
{
GtUword distance, gapcost, *Ctab, *EDtabcolumn, *Rtabcolumn, threadcount = 1;
gt_assert(scorehandler);
gt_linspaceManagement_set_ulen(spacemanager,ulen);
gapcost = gt_scorehandler_get_gapscore(scorehandler);
if (ulen == 0UL)
{
return construct_trivial_insertion_alignment(align,vlen,gapcost);
}
else if (vlen == 0UL)
{
return construct_trivial_deletion_alignment(align,ulen,gapcost);
}
else if (vlen == 1UL)
{
gt_linspaceManagement_check(spacemanager,(ulen+1)*(vlen+1)-1,ulen,
sizeof (*EDtabcolumn), sizeof (EDtabcolumn), 0);
return alignment_in_square_space_generic(spacemanager, align,
useq, ustart, ulen,
vseq, vstart, vlen, scorehandler);
}
else if (gt_linspaceManagement_checksquare(spacemanager, ulen, vlen,
sizeof (*EDtabcolumn),
sizeof (*Rtabcolumn)))
{ /* call 2dim */
return alignment_in_square_space_generic(spacemanager, align,
useq, ustart, ulen,
vseq, vstart, vlen, scorehandler);
}
#ifdef GT_THREADS_ENABLED
gt_linspaceManagement_check(spacemanager, ulen + GT_DIV2(vlen), vlen,
sizeof (*EDtabcolumn), sizeof (*Rtabcolumn),
sizeof (*Ctab));
#else
gt_linspaceManagement_check(spacemanager, ulen, vlen, sizeof (*EDtabcolumn),
sizeof (*Rtabcolumn), sizeof (*Ctab));
#endif
Ctab = gt_linspaceManagement_get_crosspointTabspace(spacemanager);
Ctab[vlen] = ulen;
distance = evaluatelinearcrosspoints(spacemanager, scorehandler,
useq, ustart, ulen,
vseq, vstart, vlen,
Ctab, 0, 0, &threadcount);
determineCtab0(Ctab, scorehandler, vseq[vstart], useq, ustart);
reconstructalignment_from_Ctab(align, Ctab, useq, ustart, vseq, vstart,
vlen, scorehandler);
return distance;
}
