, including all inherited members.
| add_byte_to_histogram(uint8_t p) | CAlphabet | |
| add_string_to_histogram(T *p, int64_t len) | CAlphabet | |
| alphabet | CAlphabet | [protected] |
| alphabet_names | CAlphabet | [static] |
| B_0 | CAlphabet | [static] |
| B_A | CAlphabet | [static] |
| B_C | CAlphabet | [static] |
| B_G | CAlphabet | [static] |
| B_T | CAlphabet | [static] |
| build_parameter_dictionary(CMap< TParameter *, CSGObject * > &dict) | CSGObject | |
| CAlphabet() | CAlphabet | |
| CAlphabet(char *alpha, int32_t len) | CAlphabet | |
| CAlphabet(EAlphabet alpha) | CAlphabet | |
| CAlphabet(CAlphabet *alpha) | CAlphabet | |
| check_alphabet(bool print_error=true) | CAlphabet | |
| check_alphabet_size(bool print_error=true) | CAlphabet | |
| clear_histogram() | CAlphabet | |
| copy_histogram(CAlphabet *src) | CAlphabet | [protected] |
| CSGObject() | CSGObject | |
| CSGObject(const CSGObject &orig) | CSGObject | |
| deep_copy() const | CSGObject | [virtual] |
| get_alphabet() const | CAlphabet | |
| get_alphabet_name(EAlphabet alphabet) | CAlphabet | [static] |
| get_global_io() | CSGObject | |
| get_global_parallel() | CSGObject | |
| get_global_version() | CSGObject | |
| get_histogram() | CAlphabet | |
| get_max_value_in_histogram() | CAlphabet | |
| get_modelsel_names() | CSGObject | |
| get_modsel_param_descr(const char *param_name) | CSGObject | |
| get_modsel_param_index(const char *param_name) | CSGObject | |
| get_name() const | CAlphabet | [virtual] |
| get_num_bits() const | CAlphabet | |
| get_num_bits_in_histogram() | CAlphabet | |
| get_num_symbols() const | CAlphabet | |
| get_num_symbols_in_histogram() | CAlphabet | |
| histogram | CAlphabet | [protected] |
| init_map_table() | CAlphabet | [protected] |
| io | CSGObject | |
| is_generic(EPrimitiveType *generic) const | CSGObject | [virtual] |
| is_valid(uint8_t c) | CAlphabet | |
| load_all_file_parameters(int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="") | CSGObject | |
| load_file_parameters(const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="") | CSGObject | |
| load_serializable(CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER) | CSGObject | [virtual] |
| load_serializable_post() | CAlphabet | [protected, virtual] |
| load_serializable_pre() | CSGObject | [protected, virtual] |
| m_hash | CSGObject | |
| m_model_selection_parameters | CSGObject | |
| m_parameter_map | CSGObject | |
| m_parameters | CSGObject | |
| map_parameters(DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos) | CSGObject | |
| maptable_to_bin | CAlphabet | [protected] |
| maptable_to_char | CAlphabet | [protected] |
| MAPTABLE_UNDEF | CAlphabet | [static] |
| migrate(DynArray< TParameter * > *param_base, const SGParamInfo *target) | CSGObject | [protected, virtual] |
| num_bits | CAlphabet | [protected] |
| num_symbols | CAlphabet | [protected] |
| one_to_one_migration_prepare(DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL) | CSGObject | [protected, virtual] |
| parallel | CSGObject | |
| print_histogram() | CAlphabet | |
| print_modsel_params() | CSGObject | |
| print_serializable(const char *prefix="") | CSGObject | [virtual] |
| remap_to_bin(uint8_t c) | CAlphabet | |
| remap_to_char(uint8_t c) | CAlphabet | |
| save_serializable(CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER) | CSGObject | [virtual] |
| save_serializable_post() | CSGObject | [protected, virtual] |
| save_serializable_pre() | CSGObject | [protected, virtual] |
| set_alphabet(EAlphabet alpha) | CAlphabet | |
| set_generic() | CSGObject | |
| set_global_io(SGIO *io) | CSGObject | |
| set_global_parallel(Parallel *parallel) | CSGObject | |
| set_global_version(Version *version) | CSGObject | |
| shallow_copy() const | CSGObject | [virtual] |
| translate_from_single_order(ST *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val) | CAlphabet | [static] |
| translate_from_single_order(ST *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap) | CAlphabet | [static] |
| translate_from_single_order(float32_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap) | CAlphabet | |
| translate_from_single_order(float64_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap) | CAlphabet | |
| translate_from_single_order(floatmax_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap) | CAlphabet | |
| translate_from_single_order_reversed(ST *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val) | CAlphabet | [static] |
| translate_from_single_order_reversed(ST *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap) | CAlphabet | [static] |
| translate_from_single_order_reversed(float32_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap) | CAlphabet | |
| translate_from_single_order_reversed(float64_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap) | CAlphabet | |
| translate_from_single_order_reversed(floatmax_t *obs, int32_t sequence_length, int32_t start, int32_t p_order, int32_t max_val, int32_t gap) | CAlphabet | |
| unset_generic() | CSGObject | |
| update_parameter_hash() | CSGObject | [protected, virtual] |
| valid_chars | CAlphabet | [protected] |
| version | CSGObject | |
| ~CAlphabet() | CAlphabet | [virtual] |
| ~CSGObject() | CSGObject | [virtual] |
