33 abs2rel =
new int[absLen+1];
36 for (i = 0; i<size && seq[i]; ++i) {
37 abs2rel[i] = baseCount;
38 if (!is_gap.
applies(seq[i])) ++baseCount;
42 for (; i <= size; ++i) {
43 abs2rel[i] = baseCount;
46 rel2abs =
new int[baseCount+1];
47 for (i = size; i>0; --i) {
66 else err =
init(gb_main, use, ref);
88 if (!gb_ref) err =
GBS_global_string(
"Your SAI '%s' has no sequence '%s/data'", ref_name, alignment_name);
void initialize(const char *seq, int size)
const char * GBS_global_string(const char *templat,...)
long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname)
static char * alignment_name
GBDATA * GBT_find_SAI(GBDATA *gb_main, const char *name)
GB_ERROR GB_await_error()
void init(const char *seq, int size)
char * GBT_get_default_ref(GBDATA *)
GBDATA * GBT_find_sequence(GBDATA *gb_species, const char *aliname)
bool is_std_gap(const char c)
char * GBT_get_default_alignment(GBDATA *gb_main)
GB_transaction ta(gb_var)
GB_CSTR GB_read_char_pntr(GBDATA *gbd)
bool applies(char c) const