GtBittab* gt_golomb_encode(GtGolomb *golomb, unsigned long x)
{
unsigned long quotient,
remain,
mask,
idx_i;
GtBittab *code;
gt_assert(golomb);
quotient = x / golomb->median;
remain = x - quotient * golomb->median;
if (golomb->len == 0) {
code = gt_bittab_new((quotient + 1) + 1);
}
else if (remain < golomb->two_pow_len - golomb->median) {
code = gt_bittab_new((quotient + 1) + (golomb->len - 1));
mask = 1UL << (golomb->len - 2);
for (idx_i = 0; idx_i < golomb->len - 1; idx_i++) {
if (remain & mask)
gt_bittab_set_bit(code, quotient + 1 + idx_i);
mask >>= 1;
}
}
void gt_string_matching_shift_and(const char *s, unsigned long n,
const char *p, unsigned long m,
ProcessMatch process_match, void *data)
{
GtBittab *D, *B[UCHAR_MAX] = { NULL };
unsigned long i, j;
gt_assert(s && p);
if (m > n || !m || !n) /* no match possible */
return;
/* preprocessing */
for (j = 0; j < m; j++) {
if (!B[(unsigned) p[j]])
B[(unsigned) p[j]] = gt_bittab_new(m);
gt_bittab_set_bit(B[(unsigned) p[j]], j);
}
/* searching */
D = gt_bittab_new(m);
for (i = 0; i < n; i++) {
gt_bittab_shift_left_equal(D);
gt_bittab_set_bit(D, 0);
if (B[(unsigned) s[i]])
gt_bittab_and_equal(D, B[(unsigned) s[i]]);
else
gt_bittab_unset(D);
if (gt_bittab_bit_is_set(D, m - 1) && process_match) {
if (process_match(i - m + 1, data))
break;
}
}
/* free */
for (i = 0; i < UCHAR_MAX; i++)
gt_bittab_delete(B[i]);
gt_bittab_delete(D);
}
static bool splice_form_is_valid(GtBittab *SA_p, const ConsensusSA *csa)
{
GtBittab *SA_p_complement; /* SA \ SA_p */
unsigned long sa, sa_prime;
bool incompatible_found, valid = true;
SA_p_complement = gt_bittab_new(csa->number_of_sas);
gt_bittab_complement(SA_p_complement, SA_p);
for (sa_prime = gt_bittab_get_first_bitnum(SA_p_complement);
sa_prime != gt_bittab_get_last_bitnum(SA_p_complement);
sa_prime = gt_bittab_get_next_bitnum(SA_p_complement, sa_prime)) {
incompatible_found = false;
for (sa = gt_bittab_get_first_bitnum(SA_p);
sa != gt_bittab_get_last_bitnum(SA_p);
sa = gt_bittab_get_next_bitnum(SA_p, sa)) {
if (!compatible(csa, sa, sa_prime)) {
incompatible_found = true;
break;
}
}
if (!incompatible_found) { valid = false; break; }
}
gt_bittab_delete(SA_p_complement);
return valid;
}
/* necessary to call consensus_sa() */
static void process_splice_form_func(GtArray *spliced_alignments_in_form,
GT_UNUSED const void *set_of_sas,
GT_UNUSED GtUword number_of_sas,
GT_UNUSED size_t size_of_sa,
void *userdata)
{
GthPGL *pgl = (GthPGL*) userdata;
GthAGS *ags;
GtBittab *assemblytab;
GtUword i;
ags = gth_ags_new(pgl);
assemblytab = gt_bittab_new(gt_array_size(pgl->saclusters));
for (i = 0; i < gt_array_size(spliced_alignments_in_form); i++) {
gt_bittab_set_bit(assemblytab, *(GtUword*)
gt_array_get(spliced_alignments_in_form, i));
}
gth_build_AGS_from_assembly(ags, assemblytab, pgl->saclusters);
gt_bittab_delete(assemblytab);
gt_array_add(pgl->assemblies, ags);
}
int encdesc_read_header(GtEncdesc *encdesc, FILE *fp, GtError *err)
{
int had_err = 0;
GtUword cur_field_num;
DescField *cur_field;
had_err = encdesc_header_io_basics(encdesc, fp, gt_io_error_fread, err);
if (!had_err)
encdesc->fields = gt_calloc((size_t) encdesc->num_of_fields,
sizeof (DescField));
for (cur_field_num = 0;
!had_err && cur_field_num < encdesc->num_of_fields;
cur_field_num++) {
cur_field = &encdesc->fields[cur_field_num];
/* cur_field->bits_per_num = 0; */
/* cur_field->prev_value = 0; */
had_err = io_field_sep_and_is_cons(cur_field, fp, gt_io_error_fread, err);
if (!had_err && cur_field->is_cons) {
had_err = io_cons_field_header(cur_field, fp, gt_io_error_fread, err);
}
else if (!had_err) {
had_err = gt_io_error_fread_one(cur_field->is_numeric, fp, err);
if (!had_err && cur_field->is_numeric) {
had_err = io_numeric_field_header(cur_field, fp, gt_io_error_fread,
err);
}
else if (!had_err) {
had_err = io_field_len_header(cur_field, fp, gt_io_error_fread, err);
if (!had_err) {
cur_field->bittab = gt_bittab_new(cur_field->len);
cur_field->data = gt_calloc((size_t) (cur_field->len + 1),
sizeof (char));
had_err = gt_io_error_fread(cur_field->data, sizeof (char),
(size_t) cur_field->len, fp, err);
}
if (!had_err)
had_err = read_field_header_bittab(cur_field, fp, err);
if (!had_err) {
cur_field->chars = gt_calloc((size_t) (cur_field->max_len + 1),
sizeof (cur_field->chars));
had_err = read_field_char_dists(cur_field, fp, err);
}
}
}
}
return had_err;
}
GtClusteredSet*
gt_clustered_set_union_find_new(GtUword num_of_elems,
GT_UNUSED GtError *err)
{
GtClusteredSet *cs;
GtClusteredSetUF *cs_uf;
cs = gt_clustered_set_create(gt_clustered_set_union_find_class());
cs_uf = (GtClusteredSetUF*) cs;
cs_uf->num_of_elems = num_of_elems;
cs_uf->cluster_elems = gt_calloc(num_of_elems, sizeof (GtClusteredSetUFElem));
cs_uf->cluster_info = gt_array_new(sizeof (GtClusteredSetUFClusterInfo));
cs_uf->in_cluster = gt_bittab_new(num_of_elems);
cs_uf->next_free_cluster_info = (GtUword) 0;
return cs;
}
static void compute_R(GtBittab **R, GtBittab **C, GtBittab **right,
unsigned long number_of_sas)
{
unsigned long sa_1, sa_2, sa_1_size = 0, sa_2_size;
long sa;
GtBittab *tmpset = gt_bittab_new(number_of_sas);
for (sa = number_of_sas-1; sa >= 0; sa--) {
sa_1 = GT_UNDEF_ULONG;
if (!gt_bittab_is_true(right[sa])) {
/* bittab is empty */
gt_bittab_equal(R[sa], C[sa]);
}
else {
for (sa_2 = gt_bittab_get_first_bitnum(right[sa]);
sa_2 != gt_bittab_get_last_bitnum(right[sa]);
sa_2 = gt_bittab_get_next_bitnum(right[sa], sa_2)) {
if (sa_1 == GT_UNDEF_ULONG) {
sa_1 = sa_2;
gt_bittab_or(tmpset, R[sa_1], C[sa]);
sa_1_size = gt_bittab_count_set_bits(tmpset);
}
else {
gt_bittab_or(tmpset, R[sa_2], C[sa]);
sa_2_size = gt_bittab_count_set_bits(tmpset);
if (sa_2_size > sa_1_size) {
sa_1 = sa_2;
sa_1_size = sa_2_size;
}
}
}
gt_assert(sa_1 != GT_UNDEF_ULONG);
gt_bittab_or(R[sa], R[sa_1], C[sa]);
}
}
gt_bittab_delete(tmpset);
}
static void compute_L(GtBittab **L, GtBittab **C, GtBittab **left,
unsigned long number_of_sas)
{
unsigned long sa, sa_1, sa_2, sa_1_size = 0, sa_2_size;
GtBittab *tmpset = gt_bittab_new(number_of_sas);
for (sa = 0; sa < number_of_sas; sa++) {
sa_1 = GT_UNDEF_ULONG;
if (!gt_bittab_is_true(left[sa])) {
/* bittab is empty */
gt_bittab_equal(L[sa], C[sa]);
}
else {
for (sa_2 = gt_bittab_get_first_bitnum(left[sa]);
sa_2 != gt_bittab_get_last_bitnum(left[sa]);
sa_2 = gt_bittab_get_next_bitnum(left[sa], sa_2)) {
if (sa_1 == GT_UNDEF_ULONG) {
sa_1 = sa_2;
gt_bittab_or(tmpset, L[sa_1], C[sa]);
sa_1_size = gt_bittab_count_set_bits(tmpset);
}
else {
gt_bittab_or(tmpset, L[sa_2], C[sa]);
sa_2_size = gt_bittab_count_set_bits(tmpset);
if (sa_2_size > sa_1_size) {
sa_1 = sa_2;
sa_1_size = sa_2_size;
}
}
}
gt_assert(sa_1 != GT_UNDEF_ULONG);
gt_bittab_or(L[sa], L[sa_1], C[sa]);
}
}
gt_bittab_delete(tmpset);
}
int gt_canvas_cairo_visit_line_pre(GtCanvas *canvas, GtLine *line,
GtError *err)
{
int had_err = 0;
double lheight, bar_vspace = BAR_VSPACE_DEFAULT,
theight = gt_graphics_get_text_height(canvas->pvt->g),
captionspace = CAPTION_BAR_SPACE_DEFAULT;
bool show_block_captions = true;
gt_assert(canvas && line);
if (gt_style_get_num(canvas->pvt->sty, "format", "block_caption_space",
&captionspace, NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_bool(canvas->pvt->sty,
"format", "show_block_captions",
&show_block_captions,
NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
had_err = gt_line_get_height(line, &lheight, canvas->pvt->sty, err);
if (!had_err) {
if (gt_style_get_num(canvas->pvt->sty,
"format", "bar_vspace",
&bar_vspace, NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_num(canvas->pvt->sty,
"format", "block_caption_font_size",
&theight, NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_line_has_captions(line) && show_block_captions)
canvas->pvt->y += theight + captionspace;
canvas->pvt->bt = gt_bittab_new(canvas->pvt->width);
gt_bittab_unset(canvas->pvt->bt);
canvas->pvt->y += lheight/2;
}
return had_err;
}
static void compute_csas(ConsensusSA *csa)
{
unsigned long i, sa_i, sa_i_size = 0, sa_prime, sa_prime_size;
GtArray *splice_form;
GtBittab **C, **left, **right, **L, **R, *U_i, *SA_i, *SA_prime;
#ifndef NDEBUG
unsigned long u_i_size, u_i_minus_1_size;
gt_assert(csa && csa->set_of_sas);
#endif
/* init sets */
C = gt_malloc(sizeof (GtBittab*) * csa->number_of_sas);
left = gt_malloc(sizeof (GtBittab*) * csa->number_of_sas);
right = gt_malloc(sizeof (GtBittab*) * csa->number_of_sas);
L = gt_malloc(sizeof (GtBittab*) * csa->number_of_sas);
R = gt_malloc(sizeof (GtBittab*) * csa->number_of_sas);
for (i = 0; i < csa->number_of_sas; i++) {
C[i] = gt_bittab_new(csa->number_of_sas);
left[i] = gt_bittab_new(csa->number_of_sas);
right[i] = gt_bittab_new(csa->number_of_sas);
L[i] = gt_bittab_new(csa->number_of_sas);
R[i] = gt_bittab_new(csa->number_of_sas);
}
U_i = gt_bittab_new(csa->number_of_sas);
SA_i = gt_bittab_new(csa->number_of_sas);
SA_prime = gt_bittab_new(csa->number_of_sas);
splice_form = gt_array_new(sizeof (unsigned long));
/* compute sets */
compute_C(C, csa);
compute_left(left, csa);
compute_right(right, csa);
compute_L(L, C, left, csa->number_of_sas);
compute_R(R, C, right, csa->number_of_sas);
/* U_0 = SA */
for (i = 0; i < csa->number_of_sas; i++)
gt_bittab_set_bit(U_i, i);
#ifndef NDEBUG
/* preparation for assertion below */
u_i_minus_1_size = gt_bittab_count_set_bits(U_i);
#endif
while (gt_bittab_is_true(U_i)) {
sa_i = GT_UNDEF_ULONG;
for (sa_prime = gt_bittab_get_first_bitnum(U_i);
sa_prime != gt_bittab_get_last_bitnum(U_i);
sa_prime = gt_bittab_get_next_bitnum(U_i, sa_prime)) {
if (sa_i == GT_UNDEF_ULONG) {
sa_i = sa_prime;
gt_bittab_or(SA_i, L[sa_i], R[sa_i]);
sa_i_size = gt_bittab_count_set_bits(SA_i);
}
else {
gt_bittab_or(SA_prime, L[sa_prime], R[sa_prime]);
sa_prime_size = gt_bittab_count_set_bits(SA_prime);
if (sa_prime_size > sa_i_size) {
sa_i = sa_prime;
sa_i_size = sa_prime_size;
gt_bittab_equal(SA_i, SA_prime);
}
}
}
/* make sure the computed splice form is maximal w.r.t. to compatibility */
gt_assert(splice_form_is_valid(SA_i, csa));
/* process splice form */
if (csa->process_splice_form) {
gt_array_reset(splice_form);
gt_bittab_get_all_bitnums(SA_i, splice_form);
csa->process_splice_form(splice_form, csa->set_of_sas, csa->number_of_sas,
csa->size_of_sa, csa->userdata);
}
/* U_i = U_i-1 \ SA_i */
gt_bittab_nand(U_i, U_i, SA_i);
#ifndef NDEBUG
/* ensure that |U_i| < |U_i-1| */
u_i_size = gt_bittab_count_set_bits(U_i);
gt_assert(u_i_size < u_i_minus_1_size);
u_i_minus_1_size = u_i_size;
#endif
}
/* free sets */
for (i = 0; i < csa->number_of_sas; i++) {
gt_bittab_delete(C[i]);
gt_bittab_delete(left[i]);
gt_bittab_delete(right[i]);
gt_bittab_delete(L[i]);
gt_bittab_delete(R[i]);
}
gt_free(C);
gt_free(left);
gt_free(right);
gt_free(L);
gt_free(R);
gt_bittab_delete(U_i);
gt_bittab_delete(SA_i);
gt_bittab_delete(SA_prime);
gt_array_delete(splice_form);
}