void gt_linearalign_check_local(GT_UNUSED bool forward,
const GtUchar *useq, GtUword ulen,
const GtUchar *vseq, GtUword vlen)
{
GtAlignment *align;
GtWord score1, score2, score3, score4,
matchscore = 2, mismatchscore = -2, gapscore = -1;
GtLinspaceManagement *spacemanager;
GtScoreHandler *scorehandler;
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(matchscore, mismatchscore, 0, gapscore);
gt_scorehandler_plain(scorehandler);
spacemanager = gt_linspace_management_new();
align = gt_alignment_new();
score1 = gt_linearalign_compute_local_generic(spacemanager, scorehandler,
align, useq, 0, ulen,
vseq, 0, vlen);
score2 = gt_alignment_eval_with_score(align, true, matchscore,
mismatchscore, gapscore);
gt_linspace_management_delete(spacemanager);
gt_scorehandler_delete(scorehandler);
if (score1 != score2)
{
fprintf(stderr,"gt_linearalign_compute_local_generic = "GT_WD" != "GT_WD
" = gt_alignment_eval_generic_with_score\n", score1, score2);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
gt_alignment_reset(align);
score3 = gt_squarealign_calculate_local(NULL, align, useq, 0, ulen,
vseq, 0, vlen, matchscore,
mismatchscore, gapscore);
if (score1 != score3)
{
fprintf(stderr,"gt_linearalign_compute_local_generic = "GT_WD" != "GT_WD
" = gt_squarealign_calculate_local\n", score1, score3);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
score4 = gt_alignment_eval_with_score(align, true, matchscore,
mismatchscore, gapscore);
if (score3 != score4)
{
fprintf(stderr,"gt_squarealign_calculate_local = "GT_WD" != "GT_WD
" = gt_alignment_eval_generic_with_score\n", score3, score4);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
gt_alignment_delete(align);
}
static int gt_linspace_align_runner(GT_UNUSED int argc,
GT_UNUSED const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments,
GtError *err)
{
GtLinspaceArguments *arguments = tool_arguments;
int had_err = 0;
GtAlignment *align;
GtWord left_dist = 0, right_dist = 0;
GtSequenceTable *sequence_table1, *sequence_table2;
GtLinspaceManagement *spacemanager;
GtScoreHandler *scorehandler = NULL;
GtTimer *linspacetimer = NULL;
GtAlphabet *alphabet = NULL;
gt_error_check(err);
gt_assert(arguments);
sequence_table1 = gt_sequence_table_new();
sequence_table2 = gt_sequence_table_new();
align = gt_alignment_new();
spacemanager = gt_linspace_management_new();
gt_linspace_management_set_TSfactor(spacemanager,arguments->timesquarefactor);
/* get sequences */
if (gt_str_array_size(arguments->strings) > 0)
{
get_onesequence(sequence_table1, arguments->strings, 0);
sequence_table1->size++;
get_onesequence(sequence_table2, arguments->strings, 1);
sequence_table2->size++;
}
else if (gt_str_array_size(arguments->files) > 0)
{
had_err = get_fastasequences(sequence_table1,
gt_str_array_get_str(arguments->files,0),err);
if (!had_err)
{
had_err = get_fastasequences(sequence_table2,
gt_str_array_get_str(arguments->files,1),err);
}
}
if (arguments->dna)
{
alphabet = gt_alphabet_new_dna();
} else
{
gt_assert(arguments->protein);
alphabet = gt_alphabet_new_protein();
}
gt_encode_sequence_table(alphabet,sequence_table1);
gt_encode_sequence_table(alphabet,sequence_table2);
if (!had_err)
{
scorehandler = gt_arguments2scorehandler(arguments,err);
if (scorehandler == NULL)
{
had_err = -1;
} else
{
if (arguments->global && arguments->protein && !arguments->has_costmatrix)
{
GtScoreHandler *costhandler = gt_scorehandler2costhandler(scorehandler);
gt_scorehandler_delete(scorehandler);
scorehandler = costhandler;
}
}
}
/* get diagonal band */
if (!had_err && arguments->diagonal)
{
if (gt_str_array_size(arguments->diagonalbonds) > 0)
{
had_err = gt_parse_score_value(__LINE__,&left_dist,
gt_str_array_get(arguments->diagonalbonds,0),
false, err);
if (!had_err)
{
had_err = gt_parse_score_value(__LINE__,&right_dist,
gt_str_array_get(arguments->diagonalbonds,1),
false, err);
}
}
}
if (!had_err && arguments->spacetime)
{
linspacetimer = gt_timer_new();
}
/* alignment functions with linear gap costs */
if (!had_err)
{
bool affine;
if (gt_str_array_size(arguments->linearcosts) > 0)
{
affine = false;
} else
{
gt_assert(gt_str_array_size(arguments->affinecosts) > 0);
affine = true;
}
had_err = gt_all_against_all_alignment_check (
affine, align, arguments,
spacemanager,
scorehandler,
gt_alphabet_characters(alphabet),
gt_alphabet_wildcard_show(alphabet),
sequence_table1,
sequence_table2,
left_dist,
right_dist,
linspacetimer,err);
}
/*spacetime option*/
if (!had_err && arguments->spacetime)
{
printf("# combined space peak in kilobytes: %f\n",
GT_KILOBYTES(gt_linspace_management_get_spacepeak(spacemanager)));
gt_timer_show_formatted(linspacetimer,"# TIME overall " GT_WD ".%02ld\n",
stdout);
}
gt_timer_delete(linspacetimer);
gt_linspace_management_delete(spacemanager);
gt_sequence_table_delete(sequence_table1);
gt_sequence_table_delete(sequence_table2);
gt_alignment_delete(align);
gt_alphabet_delete(alphabet);
gt_scorehandler_delete(scorehandler);
return had_err;
}
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);
}