SWdpresource *gt_newSWdpresource(Scoretype matchscore,
Scoretype mismatchscore,
Scoretype gapextend,
GtUword scorethreshold,
bool showalignment,
ProcessIdxMatch processmatch,
void *processmatchinfo)
{
SWdpresource *swdpresource;
swdpresource = gt_malloc(sizeof *swdpresource);
swdpresource->showalignment = showalignment;
swdpresource->scorevalues.matchscore = matchscore;
swdpresource->scorevalues.mismatchscore = mismatchscore;
swdpresource->scorevalues.gapextend = gapextend;
swdpresource->scorethreshold = scorethreshold;
swdpresource->alignment = gt_alignment_new();
swdpresource->swcol = NULL;
swdpresource->swentrycol = NULL;
swdpresource->maxedges = NULL;
swdpresource->allocatedswcol = 0;
swdpresource->allocatedmaxedges = 0;
swdpresource->processmatch = processmatch;
swdpresource->processmatchinfo = processmatchinfo;
swdpresource->dbsubstring = NULL;
swdpresource->allocateddbsubstring = 0;
return swdpresource;
}
GtAlignment* gt_alignment_new_with_seqs(const GtUchar *u, GtUword ulen,
const GtUchar *v, GtUword vlen)
{
GtAlignment *alignment;
gt_assert(u && v);
alignment = gt_alignment_new();
gt_alignment_set_seqs(alignment, u, ulen, v, vlen);
return alignment;
}
static Limdfsconstinfo *locali_allocatedfsconstinfo (GT_UNUSED
unsigned int alphasize)
{
Limdfsconstinfo *lci;
lci = gt_malloc (sizeof (Limdfsconstinfo));
lci->maxcollen = 0;
lci->tbs.alignment = gt_alignment_new();
lci->tbs.spaceGtUchardbsubstring = NULL;
lci->tbs.allocatedGtUchardbsubstring = 0;
return lci;
}
void gt_checklinearspace_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;
GtUchar *low_useq, *low_vseq;
LinspaceManagement *spacemanager;
GtScoreHandler *scorehandler;
GtAlphabet *alphabet;
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(matchscore, mismatchscore,
0, gapscore);
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();
score1 = gt_computelinearspace_local_generic(spacemanager, scorehandler,
align, useq, 0, ulen,
vseq, 0, vlen);
score2 = gt_alignment_eval_with_score(align, matchscore,
mismatchscore, gapscore);
gt_linspaceManagement_delete(spacemanager);
gt_scorehandler_delete(scorehandler);
if (score1 != score2)
{
fprintf(stderr,"gt_computelinearspace_local = "GT_WD" != "GT_WD
" = gt_alignment_eval_generic_with_score\n", score1, score2);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
gt_alignment_reset(align);
score3 = alignment_in_square_space_local(NULL, align, useq, 0, ulen,
vseq, 0, vlen, matchscore,
mismatchscore, gapscore);
if (score1 != score3)
{
fprintf(stderr,"gt_computelinearspace_local = "GT_WD" != "GT_WD
" = alignment_in_square_space_local\n", score1, score3);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
score4 = gt_alignment_eval_with_score(align, matchscore,
mismatchscore, gapscore);
if (score3 != score4)
{
fprintf(stderr,"alignment_in_square_space_local = "GT_WD" != "GT_WD
" = gt_alignment_eval_generic_with_score\n", score3, score4);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
gt_alignment_delete(align);
gt_free(low_useq);
gt_free(low_vseq);
}
static void seededmatch2alignment(const GtQuerymatch *querymatch,
GtUword querystartabsolute,
const GtEncseq *encseq,
GtQuerymatchoutoptions *querymatchoutoptions)
{
GtUword ulen, vlen, rightdistance = 0, leftdistance = 0,
offset1 = querymatchoutoptions->seedpos1 +
querymatchoutoptions->seedlen,
offset2 = querymatchoutoptions->seedpos2 +
querymatchoutoptions->seedlen;
GtAlignment *alignment = gt_alignment_new();
gt_assert(querymatch->dbstart + querymatch->dblen >= offset1);
ulen = querymatch->dbstart + querymatch->dblen - offset1;
gt_assert(querystartabsolute + querymatch->querylen >= offset2);
vlen = querystartabsolute + querymatch->querylen - offset2;
if (ulen > 0 && vlen > 0)
{
Polished_point best_polished_point = {0,0,0};
rightdistance = align_front_prune_edist(true,
&best_polished_point,
querymatchoutoptions->front_trace,
encseq,
querymatchoutoptions->ggemi,
offset1,
ulen,
offset2,
vlen);
front_trace2alignments(alignment,
querymatchoutoptions->front_trace,
&best_polished_point,
ulen,vlen);
front_trace_reset(querymatchoutoptions->front_trace,ulen+vlen);
}
gt_assert(rightdistance <= querymatch->edist);
if (querymatchoutoptions->totallength == GT_UWORD_MAX)
{
querymatchoutoptions->totallength = gt_encseq_total_length(encseq);
}
if (querymatchoutoptions->seedpos1 > querymatch->dbstart &&
querymatchoutoptions->seedpos2 > querystartabsolute)
{
Polished_point best_polished_point = {0,0,0};
ulen = querymatchoutoptions->seedpos1 - querymatch->dbstart;
vlen = querymatchoutoptions->seedpos2 - querystartabsolute;
leftdistance = align_front_prune_edist(false,
&best_polished_point,
querymatchoutoptions->front_trace,
encseq,
querymatchoutoptions->ggemi,
GT_REVERSEPOS(querymatchoutoptions->totallength,
querymatchoutoptions->seedpos1-1),
ulen,
GT_REVERSEPOS(querymatchoutoptions->totallength,
querymatchoutoptions->seedpos2-1),
vlen);
front_trace_reset(querymatchoutoptions->front_trace,ulen+vlen);
}
if (leftdistance + rightdistance > querymatch->edist)
{
fprintf(stderr,"leftdistance + rightdistance = " GT_WU " + " GT_WU " > "
GT_WU " = querymatch->edist\n",
leftdistance,rightdistance,querymatch->edist);
}
gt_assert(leftdistance + rightdistance <= querymatch->edist);
gt_alignment_delete(alignment);
}
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_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_show_seedext_runner(GT_UNUSED int argc,
GT_UNUSED const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments,
GtError *err)
{
int had_err = 0;
GtUword alignmentwidth;
GtShowSeedextArguments *arguments = tool_arguments;
GtSeedextendMatchIterator *semi;
gt_error_check(err);
gt_assert(arguments != NULL);
/* Parse option string in first line of file specified by filename. */
alignmentwidth = arguments->show_alignment ? 70 : 0;
semi = gt_seedextend_match_iterator_new(arguments->matchfilename,err);
if (semi == NULL)
{
had_err = -1;
}
/* Parse seed extensions. */
if (!had_err)
{
const GtEncseq *aencseq = gt_seedextend_match_iterator_aencseq(semi),
*bencseq = gt_seedextend_match_iterator_bencseq(semi);
GtAlignment *alignment = gt_alignment_new();
Polishing_info *pol_info = NULL;
GtSequencepairbuffer seqpairbuf = {NULL,NULL,0,0};
/* the following are used if seed_extend is set */
GtGreedyextendmatchinfo *greedyextendmatchinfo = NULL;
GtProcessinfo_and_querymatchspaceptr processinfo_and_querymatchspaceptr;
const GtUchar *characters = gt_encseq_alphabetcharacters(aencseq);
const GtUchar wildcardshow = gt_encseq_alphabetwildcardshow(aencseq);
GtUchar *alignment_show_buffer
= arguments->show_alignment ? gt_alignment_buffer_new(alignmentwidth)
: NULL;
GtLinspaceManagement *linspace_spacemanager = gt_linspaceManagement_new();
GtScoreHandler *linspace_scorehandler = gt_scorehandler_new(0,1,0,1);;
if (!arguments->relax_polish)
{
double matchscore_bias = GT_DEFAULT_MATCHSCORE_BIAS;
if (gt_seedextend_match_iterator_bias_parameters(semi))
{
matchscore_bias = gt_greedy_dna_sequence_bias_get(aencseq);
}
pol_info = polishing_info_new_with_bias(
gt_seedextend_match_iterator_errorpercentage(semi),
matchscore_bias,
gt_seedextend_match_iterator_history_size(semi));
}
if (arguments->seed_display)
{
gt_seedextend_match_iterator_seed_display_set(semi);
}
if (arguments->show_alignment || arguments->showeoplist)
{
gt_seedextend_match_iterator_querymatchoutoptions_set(semi,
true,
arguments->showeoplist,
alignmentwidth,
!arguments->relax_polish,
arguments->seed_display);
}
if (arguments->seed_extend)
{
greedyextendmatchinfo
= gt_greedy_extend_matchinfo_new(70,
GT_MAX_ALI_LEN_DIFF,
gt_seedextend_match_iterator_history_size(semi),
GT_MIN_PERC_MAT_HISTORY,
0, /* userdefinedleastlength */
GT_EXTEND_CHAR_ACCESS_ANY,
100,
pol_info);
}
if (pol_info != NULL)
{
gt_alignment_polished_ends(alignment,pol_info,false);
}
processinfo_and_querymatchspaceptr.processinfo = greedyextendmatchinfo;
if (arguments->sortmatches)
{
(void) gt_seedextend_match_iterator_all_sorted(semi,true);
}
while (true)
{
GtQuerymatch *querymatchptr = gt_seedextend_match_iterator_next(semi);
if (querymatchptr == NULL)
{
break;
}
if (gt_seedextend_match_iterator_has_seedline(semi))
{
if (arguments->seed_extend)
{
if (aencseq == bencseq)
{
const GtUword
seedlen = gt_seedextend_match_iterator_seedlen(semi),
seedpos1 = gt_seedextend_match_iterator_seedpos1(semi),
seedpos2 = gt_seedextend_match_iterator_seedpos2(semi);
processinfo_and_querymatchspaceptr.querymatchspaceptr
= querymatchptr;
had_err = gt_greedy_extend_selfmatch_with_output(
&processinfo_and_querymatchspaceptr,
aencseq,
seedlen,
seedpos1,
seedpos2,
err);
if (had_err)
{
break;
}
} else
{
gt_assert(false);
}
} else
{
const GtUword query_totallength
= gt_encseq_seqlength(bencseq,
gt_querymatch_queryseqnum(querymatchptr));
gt_show_seed_extend_encseq(querymatchptr,
aencseq,
bencseq,
query_totallength);
}
} else
{
gt_show_seed_extend_plain(&seqpairbuf,
linspace_spacemanager,
linspace_scorehandler,
alignment,
alignment_show_buffer,
alignmentwidth,
arguments->showeoplist,
characters,
wildcardshow,
aencseq,
bencseq,
querymatchptr);
}
}
polishing_info_delete(pol_info);
gt_greedy_extend_matchinfo_delete(greedyextendmatchinfo);
gt_free(alignment_show_buffer);
gt_scorehandler_delete(linspace_scorehandler);
gt_linspaceManagement_delete(linspace_spacemanager);
gt_free(seqpairbuf.a_sequence);
gt_free(seqpairbuf.b_sequence);
gt_alignment_delete(alignment);
}
gt_seedextend_match_iterator_delete(semi);
return had_err;
}
void gt_template_utils_setup(void) {
source = gt_template_new();
alignment = gt_alignment_new();
target = gt_template_new();
output_attributes = gt_output_map_attributes_new();
}
