, including all inherited members.
| add_example_to_tree_mismatch_recursion(int32_t tree, int32_t i, float64_t alpha, int32_t *vec, int32_t len_rem, int32_t degree_rec, int32_t mismatch_rec, int32_t max_mismatch, float64_t *weights) | CTrie< Trie > | |
| add_to_trie(int32_t i, int32_t seq_offset, int32_t *vec, float32_t alpha, float64_t *weights, bool degree_times_position_weights) | CTrie< Trie > | |
| check_treemem() | CTrie< Trie > | |
| compact_nodes(int32_t start_node, int32_t depth, float64_t *weights) | CTrie< Trie > | |
| compare(const CTrie &other) | CTrie< Trie > | |
| compare_traverse(int32_t node, const CTrie &other, int32_t other_node) | CTrie< Trie > | |
| compute_abs_weights(int32_t &len) | CTrie< Trie > | |
| compute_abs_weights_tree(int32_t tree, int32_t depth) | CTrie< Trie > | |
| compute_by_tree_helper(int32_t *vec, int32_t len, int32_t seq_pos, int32_t tree_pos, int32_t weight_pos, float64_t *weights, bool degree_times_position_weights) | CTrie< Trie > | |
| compute_by_tree_helper(int32_t *vec, int32_t len, int32_t seq_pos, int32_t tree_pos, int32_t weight_pos, float64_t *LevelContrib, float64_t factor, int32_t mkl_stepsize, float64_t *weights, bool degree_times_position_weights) | CTrie< Trie > | |
| compute_scoring_helper(int32_t tree, int32_t i, int32_t j, float64_t weight, int32_t d, int32_t max_degree, int32_t num_feat, int32_t num_sym, int32_t sym_offset, int32_t offs, float64_t *result) | CTrie< Trie > | |
| count(const float64_t w, const int32_t depth, const struct TreeParseInfo info, const int32_t p, int32_t *x, const int32_t k) | CTrie< Trie > | |
| create(int32_t len, bool p_use_compact_terminal_nodes=true) | CTrie< Trie > | |
| CSGObject() | CSGObject | |
| CSGObject(const CSGObject &orig) | CSGObject | |
| CTrie() | CTrie< Trie > | |
| CTrie(int32_t d, bool p_use_compact_terminal_nodes=true) | CTrie< Trie > | |
| CTrie(const CTrie &to_copy) | CTrie< Trie > | |
| degree | CTrie< Trie > | [protected] |
| delete_trees(bool p_use_compact_terminal_nodes=true) | CTrie< Trie > | |
| destroy() | CTrie< Trie > | |
| display_node(int32_t node) const | CTrie< Trie > | |
| fill_backtracking_table(int32_t pos, DynArray< ConsensusEntry > *prev, DynArray< ConsensusEntry > *cur, bool cumulative, float64_t *weights) | CTrie< Trie > | |
| fill_backtracking_table_recursion(Trie *tree, int32_t depth, uint64_t seq, float64_t value, DynArray< ConsensusEntry > *table, float64_t *weights) | CTrie< Trie > | |
| find_deepest_node(int32_t start_node, int32_t &deepest_node) const | CTrie< Trie > | |
| find_node(int32_t node, int32_t *trace, int32_t &trace_len) const | CTrie< Trie > | |
| get_cumulative_score(int32_t pos, uint64_t seq, int32_t deg, float64_t *weights) | CTrie< Trie > | |
| get_io() | CSGObject | |
| get_name() const | CTrie< Trie > | [virtual] |
| get_node(bool last_node=false) | CTrie< Trie > | |
| get_num_used_nodes() | CTrie< Trie > | |
| get_parallel() | CSGObject | |
| get_use_compact_terminal_nodes() | CTrie< Trie > | |
| get_version() | CSGObject | |
| get_weights_in_tree() | CTrie< Trie > | |
| io | CSGObject | |
| is_generic(EPrimitiveType *generic) const | CSGObject | [virtual] |
| length | CTrie< Trie > | [protected] |
| load_serializable(CSerializableFile *file, const char *prefix="") | CSGObject | [virtual] |
| load_serializable_post() | CSGObject | [protected, virtual] |
| load_serializable_pre() | CSGObject | [protected, virtual] |
| m_parameters | CSGObject | [protected] |
| nofsKmers | CTrie< Trie > | [protected] |
| NUM_SYMS | CTrie< Trie > | |
| operator=(const CTrie &to_copy) | CTrie< Trie > | |
| parallel | CSGObject | |
| POIMs_add_SLR(float64_t *const *const poims, const int32_t K, const int32_t debug) | CTrie< Trie > | |
| POIMs_add_SLR(float64_t *const *const poims, const int32_t K, const int32_t debug) | CTrie< Trie > | |
| POIMs_add_SLR_helper1(const int32_t nodeIdx, const int32_t depth, const int32_t i, const int32_t y0, float64_t *const *const poims, const int32_t K, const int32_t debug) | CTrie< Trie > | |
| POIMs_add_SLR_helper1(const int32_t nodeIdx, const int32_t depth, const int32_t i, const int32_t y0, float64_t *const *const poims, const int32_t K, const int32_t debug) | CTrie< Trie > | |
| POIMs_add_SLR_helper2(float64_t *const *const poims, const int32_t K, const int32_t k, const int32_t i, const int32_t y, const float64_t valW, const float64_t valS, const float64_t valL, const float64_t valR, const int32_t debug) | CTrie< Trie > | |
| POIMs_add_SLR_helper2(float64_t *const *const poims, const int32_t K, const int32_t k, const int32_t i, const int32_t y, const float64_t valW, const float64_t valS, const float64_t valL, const float64_t valR, const int32_t debug) | CTrie< Trie > | |
| POIMs_calc_SLR_helper1(const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, int32_t const lastSym, float64_t *S, float64_t *L, float64_t *R) | CTrie< Trie > | |
| POIMs_calc_SLR_helper1(const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, int32_t const lastSym, float64_t *S, float64_t *L, float64_t *R) | CTrie< Trie > | |
| POIMs_calc_SLR_helper2(const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, float64_t *S, float64_t *L, float64_t *R) | CTrie< Trie > | |
| POIMs_calc_SLR_helper2(const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, float64_t *S, float64_t *L, float64_t *R) | CTrie< Trie > | |
| POIMs_extract_W(float64_t *const *const W, const int32_t K) | CTrie< Trie > | |
| POIMs_extract_W(float64_t *const *const W, const int32_t K) | CTrie< Trie > | |
| POIMs_extract_W_helper(const int32_t nodeIdx, const int32_t depth, const int32_t offset, const int32_t y0, float64_t *const *const W, const int32_t K) | CTrie< Trie > | |
| POIMs_extract_W_helper(const int32_t nodeIdx, const int32_t depth, const int32_t offset, const int32_t y0, float64_t *const *const W, const int32_t K) | CTrie< Trie > | |
| POIMs_get_SLR(const int32_t parentIdx, const int32_t sym, const int32_t depth, float64_t *S, float64_t *L, float64_t *R) | CTrie< Trie > | |
| POIMs_get_SLR(const int32_t parentIdx, const int32_t sym, const int32_t depth, float64_t *S, float64_t *L, float64_t *R) | CTrie< Trie > | |
| POIMs_precalc_SLR(const float64_t *const distrib) | CTrie< Trie > | |
| POIMs_precalc_SLR(const float64_t *const distrib) | CTrie< Trie > | |
| position_weights | CTrie< Trie > | [protected] |
| print_serializable(const char *prefix="") | CSGObject | [virtual] |
| save_serializable(CSerializableFile *file, const char *prefix="") | CSGObject | [virtual] |
| save_serializable_post() | CSGObject | [protected, virtual] |
| save_serializable_pre() | CSGObject | [protected, virtual] |
| set_degree(int32_t d) | CTrie< Trie > | |
| set_generic() | CSGObject | |
| set_io(IO *io) | CSGObject | |
| set_parallel(Parallel *parallel) | CSGObject | |
| set_position_weights(const float64_t *p_position_weights) | CTrie< Trie > | |
| set_use_compact_terminal_nodes(bool p_use_compact_terminal_nodes) | CTrie< Trie > | |
| set_version(Version *version) | CSGObject | |
| set_weights_in_tree(bool weights_in_tree_) | CTrie< Trie > | |
| traverse(int32_t tree, const int32_t p, struct TreeParseInfo info, const int32_t depth, int32_t *const x, const int32_t k) | CTrie< Trie > | |
| TreeMem | CTrie< Trie > | [protected] |
| TreeMemPtr | CTrie< Trie > | [protected] |
| TreeMemPtrMax | CTrie< Trie > | [protected] |
| trees | CTrie< Trie > | [protected] |
| unset_generic() | CSGObject | |
| use_compact_terminal_nodes | CTrie< Trie > | [protected] |
| version | CSGObject | |
| weights_in_tree | CTrie< Trie > | [protected] |
| ~CSGObject() | CSGObject | [virtual] |
| ~CTrie() | CTrie< Trie > | [virtual] |
