/* global alignment with linear gapcosts in linear space */
GtUword gt_computelinearspace_generic(LinspaceManagement *spacemanager,
GtScoreHandler *scorehandler,
GtAlignment *align,
const GtUchar *useq,
GtUword ustart,
GtUword ulen,
const GtUchar *vseq,
GtUword vstart,
GtUword vlen)
{
GtUword distance;
gt_assert(spacemanager && scorehandler && align);
gt_alignment_set_seqs(align, useq+ustart, ulen, vseq+vstart, vlen);
distance = gt_calc_linearalign(spacemanager, scorehandler, align,
useq, ustart, ulen,
vseq, vstart, vlen);
return distance;
}
void gt_checklinearspace(GT_UNUSED bool forward,
const GtUchar *useq,
GtUword ulen,
const GtUchar *vseq,
GtUword vlen)
{
GtAlignment *align;
GtUword edist1, edist2, edist3, edist4,
matchcost = 0, mismatchcost = 1, gapcost = 1;
LinspaceManagement *spacemanager;
GtScoreHandler *scorehandler;
GtUchar *low_useq, *low_vseq;
if (memchr(useq, LINEAR_EDIST_GAP,ulen) != NULL)
{
fprintf(stderr,"%s: sequence u contains gap symbol\n",__func__);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
if (memchr(vseq, LINEAR_EDIST_GAP,vlen) != NULL)
{
fprintf(stderr,"%s: sequence v contains gap symbol\n",__func__);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
scorehandler = gt_scorehandler_new_DNA(matchcost, mismatchcost, 0, gapcost);
GtAlphabet *alphabet = gt_scorehandler_get_alphabet(scorehandler);
low_useq = check_dna_sequence(useq, ulen, alphabet);
low_vseq = check_dna_sequence(vseq, vlen, alphabet);
if (low_useq == NULL || low_vseq == NULL)
{
low_useq? gt_free(low_useq):0;
low_vseq? gt_free(low_vseq):0;
gt_scorehandler_delete(scorehandler);
return;
}
spacemanager = gt_linspaceManagement_new();
align = gt_alignment_new_with_seqs(low_useq, ulen, low_vseq, vlen);
edist1 = gt_calc_linearalign(spacemanager, scorehandler, align,
low_useq, 0, ulen,
low_vseq, 0, vlen);
edist2 = distance_only_global_alignment(useq, 0, ulen, vseq, 0, vlen,
scorehandler);
if (edist1 != edist2)
{
fprintf(stderr,"gt_calc_linearalign = "GT_WU" != "GT_WU
" = distance_only_global_alignment\n", edist1,edist2);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
edist3 = gt_alignment_eval_with_score(align, matchcost,
mismatchcost, gapcost);
if (edist2 != edist3)
{
fprintf(stderr,"distance_only_global_alignment = "GT_WU" != "GT_WU
" = gt_alignment_eval_with_score\n", edist2,edist3);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
edist4 = gt_calc_linearedist(low_useq, ulen, low_vseq, vlen);
if (edist3 != edist4)
{
fprintf(stderr,"gt_alignment_eval_with_score = "GT_WU" != "GT_WU
" = gt_calc_linearedist\n", edist3, edist4);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
gt_free(low_useq);
gt_free(low_vseq);
gt_linspaceManagement_delete(spacemanager);
gt_scorehandler_delete(scorehandler);
gt_alignment_delete(align);
}
/* 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;
}
void gt_linearalign_check(GT_UNUSED bool forward,
const GtUchar *useq,
GtUword ulen,
const GtUchar *vseq,
GtUword vlen)
{
GtAlignment *align;
GtUword edist1, edist2, edist3, edist4,
matchcost = 0, mismatchcost = 1, gapcost = 1;
GtLinspaceManagement *spacemanager;
GtScoreHandler *scorehandler;
const bool downcase = true;
if (memchr(useq, LINEAR_EDIST_GAP,ulen) != NULL)
{
fprintf(stderr,"%s: sequence u contains gap symbol\n",__func__);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
if (memchr(vseq, LINEAR_EDIST_GAP,vlen) != NULL)
{
fprintf(stderr,"%s: sequence v contains gap symbol\n",__func__);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
scorehandler = gt_scorehandler_new(matchcost, mismatchcost, 0, gapcost);
gt_scorehandler_plain(scorehandler);
gt_scorehandler_downcase(scorehandler);
spacemanager = gt_linspace_management_new();
align = gt_alignment_new_with_seqs(useq, ulen, vseq, vlen);
edist1 = gt_calc_linearalign(spacemanager, scorehandler, align,
useq, 0, ulen,
vseq, 0, vlen);
edist2 = gt_squarealign_global_distance_only(useq, 0, ulen, vseq, 0, vlen,
scorehandler);
if (edist1 != edist2)
{
fprintf(stderr,"gt_calc_linearalign = "GT_WU" != "GT_WU
" = gt_squarealign_global_distance_only\n", edist1,edist2);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
edist3 = gt_alignment_eval_with_score(align, true, matchcost,
mismatchcost, gapcost);
if (edist2 != edist3)
{
fprintf(stderr,"gt_squarealign_global_distance_only = "GT_WU" != "GT_WU
" = gt_alignment_eval_with_score\n", edist2,edist3);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
edist4 = gt_calc_linearedist(downcase,useq, ulen, vseq, vlen);
if (edist3 != edist4)
{
fprintf(stderr,"gt_alignment_eval_with_score = "GT_WU" != "GT_WU
" = gt_calc_linearedist\n", edist3, edist4);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
gt_linspace_management_delete(spacemanager);
gt_scorehandler_delete(scorehandler);
gt_alignment_delete(align);
}
