, including all inherited members.
| add_example_to_tree_mismatch_recursion(INT tree, INT i, DREAL alpha, INT *vec, INT len_rem, INT degree_rec, INT mismatch_rec, INT max_mismatch, DREAL *weights) | CTrie< Trie > | |
| add_to_trie(int i, INT seq_offset, INT *vec, float alpha, DREAL *weights, bool degree_times_position_weights) | CTrie< Trie > | |
| check_treemem() | CTrie< Trie > | |
| compact_nodes(INT start_node, INT depth, DREAL *weights) | CTrie< Trie > | |
| compare(const CTrie &other) | CTrie< Trie > | |
| compare_traverse(INT node, const CTrie &other, INT other_node) | CTrie< Trie > | |
| compute_abs_weights(int &len) | CTrie< Trie > | |
| compute_abs_weights_tree(INT tree, INT depth) | CTrie< Trie > | |
| compute_by_tree_helper(INT *vec, INT len, INT seq_pos, INT tree_pos, INT weight_pos, DREAL *weights, bool degree_times_position_weights) | CTrie< Trie > | |
| compute_by_tree_helper(INT *vec, INT len, INT seq_pos, INT tree_pos, INT weight_pos, DREAL *LevelContrib, DREAL factor, INT mkl_stepsize, DREAL *weights, bool degree_times_position_weights) | CTrie< Trie > | |
| compute_scoring_helper(INT tree, INT i, INT j, DREAL weight, INT d, INT max_degree, INT num_feat, INT num_sym, INT sym_offset, INT offs, DREAL *result) | CTrie< Trie > | |
| count(const DREAL w, const INT depth, const struct TreeParseInfo info, const INT p, INT *x, const INT k) | CTrie< Trie > | |
| create(INT len, bool p_use_compact_terminal_nodes=true) | CTrie< Trie > | |
| CSGObject() | CSGObject | |
| CSGObject(const CSGObject &orig) | CSGObject | |
| CTrie(INT 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(INT node) const | CTrie< Trie > | |
| fill_backtracking_table(INT pos, CDynamicArray< ConsensusEntry > *prev, CDynamicArray< ConsensusEntry > *cur, bool cumulative, DREAL *weights) | CTrie< Trie > | |
| fill_backtracking_table_recursion(Trie *tree, INT depth, ULONG seq, DREAL value, CDynamicArray< ConsensusEntry > *table, DREAL *weights) | CTrie< Trie > | |
| find_deepest_node(INT start_node, INT &deepest_node) const | CTrie< Trie > | |
| find_node(INT node, INT *trace, INT &trace_len) const | CTrie< Trie > | |
| get_cumulative_score(INT pos, ULONG seq, INT deg, DREAL *weights) | CTrie< Trie > | |
| get_node(bool last_node=false) | CTrie< Trie > | |
| get_num_used_nodes() | CTrie< Trie > | |
| get_use_compact_terminal_nodes() | CTrie< Trie > | |
| get_weights_in_tree() | CTrie< Trie > | |
| io | CSGObject | [static] |
| length | CTrie< Trie > | [protected] |
| nofsKmers | CTrie< Trie > | [protected] |
| NUM_SYMS | CTrie< Trie > | |
| operator=(const CTrie &to_copy) | CTrie< Trie > | |
| parallel | CSGObject | [static] |
| POIMs_add_SLR(DREAL *const *const poims, const INT K, const INT debug) | CTrie< Trie > | |
| POIMs_add_SLR_helper1(const INT nodeIdx, const int depth, const INT i, const INT y0, DREAL *const *const poims, const INT K, const INT debug) | CTrie< Trie > | |
| POIMs_add_SLR_helper2(DREAL *const *const poims, const int K, const int k, const INT i, const INT y, const DREAL valW, const DREAL valS, const DREAL valL, const DREAL valR, const INT debug) | CTrie< Trie > | |
| POIMs_calc_SLR_helper1(const DREAL *const distrib, const INT i, const INT nodeIdx, INT left_tries_idx[4], const int depth, INT const lastSym, DREAL *S, DREAL *L, DREAL *R) | CTrie< Trie > | |
| POIMs_calc_SLR_helper2(const DREAL *const distrib, const INT i, const INT nodeIdx, INT left_tries_idx[4], const int depth, DREAL *S, DREAL *L, DREAL *R) | CTrie< Trie > | |
| POIMs_extract_W(DREAL *const *const W, const INT K) | CTrie< Trie > | |
| POIMs_extract_W_helper(const INT nodeIdx, const int depth, const INT offset, const INT y0, DREAL *const *const W, const INT K) | CTrie< Trie > | |
| POIMs_get_SLR(const INT parentIdx, const INT sym, const int depth, DREAL *S, DREAL *L, DREAL *R) | CTrie< Trie > | |
| POIMs_precalc_SLR(const DREAL *const distrib) | CTrie< Trie > | |
| position_weights | CTrie< Trie > | [protected] |
| set_degree(INT d) | CTrie< Trie > | |
| set_position_weights(const DREAL *p_position_weights) | CTrie< Trie > | |
| set_use_compact_terminal_nodes(bool p_use_compact_terminal_nodes) | CTrie< Trie > | |
| set_weights_in_tree(bool weights_in_tree_) | CTrie< Trie > | |
| traverse(INT tree, const INT p, struct TreeParseInfo info, const INT depth, INT *const x, const INT k) | CTrie< Trie > | |
| TreeMem | CTrie< Trie > | [protected] |
| TreeMemPtr | CTrie< Trie > | [protected] |
| TreeMemPtrMax | CTrie< Trie > | [protected] |
| trees | CTrie< Trie > | [protected] |
| use_compact_terminal_nodes | CTrie< Trie > | [protected] |
| version | CSGObject | [static] |
| weights_in_tree | CTrie< Trie > | [protected] |
| ~CSGObject() | CSGObject | [virtual] |
| ~CTrie() | CTrie< Trie > | |