| 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_gradient_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 | |
| clone() | CSGObject | virtual |
| copy_histogram(CAlphabet *src) | CAlphabet | protected |
| CSGObject() | CSGObject | |
| CSGObject(const CSGObject &orig) | CSGObject | |
| deep_copy() const | CSGObject | virtual |
| equals(CSGObject *other, float64_t accuracy=0.0, bool tolerant=false) | 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_serializable(CSerializableFile *file, const char *prefix="") | CSGObject | virtual |
| load_serializable_post() | CAlphabet | protectedvirtual |
| load_serializable_pre() | CSGObject | protectedvirtual |
| m_gradient_parameters | CSGObject | |
| m_hash | CSGObject | |
| m_model_selection_parameters | CSGObject | |
| m_parameters | CSGObject | |
| maptable_to_bin | CAlphabet | protected |
| maptable_to_char | CAlphabet | protected |
| MAPTABLE_UNDEF | CAlphabet | static |
| num_bits | CAlphabet | protected |
| num_symbols | CAlphabet | protected |
| parallel | CSGObject | |
| parameter_hash_changed() | CSGObject | virtual |
| 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="") | CSGObject | virtual |
| save_serializable_post() | CSGObject | protectedvirtual |
| save_serializable_pre() | CSGObject | protectedvirtual |
| set_alphabet(EAlphabet alpha) | CAlphabet | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| set_generic() | CSGObject | |
| 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 | virtual |
| valid_chars | CAlphabet | protected |
| version | CSGObject | |
| ~CAlphabet() | CAlphabet | virtual |
| ~CSGObject() | CSGObject | virtual |
