, 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] |
| 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 | |
| get_alphabet() const | CAlphabet | |
| get_alphabet_name(EAlphabet alphabet) | CAlphabet | [static] |
| get_hist(int64_t **h, int32_t *len) | CAlphabet | |
| get_histogram() | CAlphabet | |
| get_io() | CSGObject | |
| get_max_value_in_histogram() | CAlphabet | |
| 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 | |
| get_parallel() | CSGObject | |
| get_version() | CSGObject | |
| 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(void) | CAlphabet | [protected, virtual] |
| load_serializable_pre() | CSGObject | [protected, virtual] |
| m_parameters | CSGObject | [protected] |
| maptable_to_bin | CAlphabet | [protected] |
| maptable_to_char | CAlphabet | [protected] |
| MAPTABLE_UNDEF | CAlphabet | [static] |
| num_bits | CAlphabet | [protected] |
| num_symbols | CAlphabet | [protected] |
| parallel | CSGObject | |
| print_histogram() | CAlphabet | |
| 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 | [protected, virtual] |
| save_serializable_pre() | CSGObject | [protected, virtual] |
| set_alphabet(EAlphabet alpha) | CAlphabet | |
| set_generic() | CSGObject | |
| set_io(IO *io) | CSGObject | |
| set_parallel(Parallel *parallel) | CSGObject | |
| set_version(Version *version) | CSGObject | |
| 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_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] |
| unset_generic() | CSGObject | |
| valid_chars | CAlphabet | [protected] |
| version | CSGObject | |
| ~CAlphabet() | CAlphabet | [virtual] |
| ~CSGObject() | CSGObject | [virtual] |
