static Gtmaxcoordvalue *evaluateallLScolumns(LinspaceManagement *spacemanager,
GtScoreHandler *scorehandler,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen)
{
GtUword colindex;
GtWord *Ltabcolumn;
GtUwordPair *Starttabcolumn;
Gtmaxcoordvalue *max;
Ltabcolumn = gt_linspaceManagement_get_valueTabspace(spacemanager);
Starttabcolumn = gt_linspaceManagement_get_rTabspace(spacemanager);
firstLStabcolumn(Ltabcolumn, Starttabcolumn, ulen);
max = gt_linspaceManagement_get_maxspace(spacemanager);
for (colindex = 1UL; colindex <= vlen; colindex++)
{
nextLStabcolumn(Ltabcolumn, Starttabcolumn, scorehandler,
useq, ustart, ulen, vseq[vstart+colindex-1], colindex, max);
}
return max;
}
/* create an local alignment in square space, 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_generic(GtLinspaceManagement
*spacemanager,
GtAlignment *align,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen,
const GtScoreHandler
*scorehandler)
{
GtWord score = 0, **Ltabcolumn;
GtMaxcoordvalue *max;
gt_assert(align != NULL);
if (spacemanager == NULL)
{
/*use it in normally case*/
gt_array2dim_malloc(Ltabcolumn, (ulen+1), (vlen+1));
max = gt_max_new();
}
else
{
/*use it in lineraspace context*/
Ltabcolumn = (GtWord **)
gt_linspaceManagement_change_to_square(spacemanager,ulen,vlen);
max = gt_linspaceManagement_get_maxspace(spacemanager);
}
score = fillDPtab_in_square_space_local(Ltabcolumn, max, useq, ustart, ulen,
vseq, vstart, vlen, scorehandler);
/* reconstruct local alignment from 2dimarray Ltabcolumn */
reconstructalignment_from_Ltab(align, Ltabcolumn, max,
useq, ustart, ulen,
vseq,vstart,vlen,scorehandler);
if (gt_max_get_length_safe(max))
{
ustart = ustart+(gt_max_get_start(max)).a;
vstart = vstart+(gt_max_get_start(max)).b;
ulen = gt_max_get_row_length(max);
vlen = gt_max_get_col_length(max);
gt_alignment_set_seqs(align, &useq[ustart], ulen,
&vseq[vstart], vlen);
}
if (spacemanager == NULL)
{
gt_array2dim_delete(Ltabcolumn);
gt_max_delete(max);
}
return score;
}
