, 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 > | |