void gt_print_edist_alignment(const GtUchar *useq, GtUword ustart, GtUword ulen,
const GtUchar *vseq, GtUword vstart, GtUword vlen)
{
GtAlignment *align;
align = gt_alignment_new_with_seqs(useq+ustart, ulen, vseq+vstart, vlen);
alignment_in_square_space(NULL, align, useq, ustart, ulen,
vseq, vstart, vlen, 0, 1, 1);
gt_alignment_show(align, true, stdout, 80);
gt_alignment_delete(align);
}
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);
}
gt_alignment_show(align,stdout,80);
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);
}