14 #ifndef AP_PRO_A_NUCS_HXX
23 #ifndef AP_SEQ_DNA_HXX
26 #ifndef AP_SEQ_SIMPLE_PRO_HXX
29 #ifndef _GLIBCXX_STRING
33 #define di_assert(cond) arb_assert(cond)
35 #define AWAR_DIST_PREFIX "dist/"
36 #define AWAR_DIST_CORR_TRANS AWAR_DIST_PREFIX "correction/trans"
37 #define AWAR_DIST_SAVE_MATRIX_BASE "tmp/" AWAR_DIST_PREFIX "save_matrix"
39 #define AWAR_DIST_DIST_PREFIX AWAR_DIST_PREFIX "dist/"
40 #define AWAR_DIST_MIN_DIST AWAR_DIST_DIST_PREFIX "lower"
41 #define AWAR_DIST_MAX_DIST AWAR_DIST_DIST_PREFIX "upper"
106 bool tree_contains_dups;
112 tree_contains_dups =
true;
116 insert_in_hash(tree->get_rightson());
117 insert_in_hash(tree->get_leftson());
139 char cancel_columns[256];
140 size_t allocated_entries;
144 double corr(
double dist,
double b,
double & sigma);
145 char *calculate_overall_freqs(
double rel_frequencies[
AP_MAX],
char *cancel_columns);
179 void announce_change() {
if (changed_cb) changed_cb(); }
181 void forget_no_announce() {
186 void set(
DI_MATRIX *new_global) {
di_assert(!matrix); matrix = new_global; announce_change(); }
195 forget_no_announce();
219 if (matrix && matrix->
matrix_type != wanted_type) {
236 #error di_matr.hxx included twice
237 #endif // DI_MATR_HXX
AW_window * DI_create_save_matrix_window(AW_root *aw_root, save_matrix_params *save_params)
const char * get_aliname() const
long GBS_write_hash(GB_HASH *hs, const char *key, long val)
return string(buffer, length)
void show_warnings(const string &helpfile)
GB_ERROR extract_from_tree(const char *treename, bool *aborted_flag)
bool has_type(DI_MATRIX_TYPE type) const
DI_ENTRY(GBDATA *gbd, DI_MATRIX *phmatrix_)
int get_index(const char *name) const
GB_ERROR calculate_pro(DI_TRANSFORMATION transformation, bool *aborted_flag)
GB_ERROR calculate(const char *cancel, DI_TRANSFORMATION transformation, bool *aborted_flag, AP_matrix *userdef_matrix)
AP_sequence_parsimony * get_nucl_seq()
void GBS_free_hash(GB_HASH *hs)
void set_changed_cb(DI_MATRIX_CB cb)
#define DOWNCAST(totype, expr)
void forget_if_not_has_type(DI_MATRIX_TYPE wanted_type)
void applyTo(struct TreeOrderedSpecies **gb_species_array, size_t array_size) const
const AliView * get_aliview() const
DI_MATRIX(const AliView &aliview)
DI_MATRIX_TYPE matrix_type
DI_GLOBAL_MATRIX GLOBAL_MATRIX
const WeightedFilter * weighted_filter
MatrixOrder(GBDATA *gb_main, GB_CSTR sort_tree_name)
AP_sequence_simple_protein * get_prot_seq()
#define __ATTR__USERESULT
void replaceBy(DI_MATRIX *new_global)
DI_TRANSFORMATION detect_transformation(std::string &msg)
const char * get_aliname() const
const char * save(const char *filename, enum DI_SAVE_TYPE type)
char * compress(TreeNode *tree)
DI_MATRIX * swap(DI_MATRIX *other)
GB_ERROR load(LoadWhat what, const MatrixOrder &order, bool show_warnings, GBDATA **species_list) __ATTR__USERESULT
GBDATA * get_gb_main() const
long GBS_read_hash(const GB_HASH *hs, const char *key)