Definition at line 134 of file Trie.h.
Public Member Functions | |
CTrie (INT d, bool p_use_compact_terminal_nodes=true) | |
CTrie (const CTrie &to_copy) | |
~CTrie () | |
const CTrie & | operator= (const CTrie &to_copy) |
bool | compare_traverse (INT node, const CTrie &other, INT other_node) |
bool | compare (const CTrie &other) |
bool | find_node (INT node, INT *trace, INT &trace_len) const |
INT | find_deepest_node (INT start_node, INT &deepest_node) const |
void | display_node (INT node) const |
void | destroy () |
void | set_degree (INT d) |
void | create (INT len, bool p_use_compact_terminal_nodes=true) |
void | delete_trees (bool p_use_compact_terminal_nodes=true) |
void | add_to_trie (int i, INT seq_offset, INT *vec, float alpha, DREAL *weights, bool degree_times_position_weights) |
DREAL | compute_abs_weights_tree (INT tree, INT depth) |
DREAL * | compute_abs_weights (int &len) |
DREAL | compute_by_tree_helper (INT *vec, INT len, INT seq_pos, INT tree_pos, INT weight_pos, DREAL *weights, bool degree_times_position_weights) |
void | 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) |
void | 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) |
void | 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) |
void | traverse (INT tree, const INT p, struct TreeParseInfo info, const INT depth, INT *const x, const INT k) |
void | count (const DREAL w, const INT depth, const struct TreeParseInfo info, const INT p, INT *x, const INT k) |
INT | compact_nodes (INT start_node, INT depth, DREAL *weights) |
DREAL | get_cumulative_score (INT pos, ULONG seq, INT deg, DREAL *weights) |
void | fill_backtracking_table_recursion (Trie *tree, INT depth, ULONG seq, DREAL value, CDynamicArray< ConsensusEntry > *table, DREAL *weights) |
void | fill_backtracking_table (INT pos, CDynamicArray< ConsensusEntry > *prev, CDynamicArray< ConsensusEntry > *cur, bool cumulative, DREAL *weights) |
void | POIMs_extract_W (DREAL *const *const W, const INT K) |
void | POIMs_precalc_SLR (const DREAL *const distrib) |
void | POIMs_get_SLR (const INT parentIdx, const INT sym, const int depth, DREAL *S, DREAL *L, DREAL *R) |
void | POIMs_add_SLR (DREAL *const *const poims, const INT K, const INT debug) |
bool | get_use_compact_terminal_nodes () |
void | set_use_compact_terminal_nodes (bool p_use_compact_terminal_nodes) |
INT | get_num_used_nodes () |
void | set_position_weights (const DREAL *p_position_weights) |
INT | get_node (bool last_node=false) |
void | check_treemem () |
void | set_weights_in_tree (bool weights_in_tree_) |
bool | get_weights_in_tree () |
void | POIMs_extract_W_helper (const INT nodeIdx, const int depth, const INT offset, const INT y0, DREAL *const *const W, const INT K) |
void | 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) |
void | 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) |
void | 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) |
void | 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) |
Public Attributes | |
INT | NUM_SYMS |
Static Public Attributes | |
static CParallel | parallel |
static CIO | io |
static CVersion | version |
Protected Attributes | |
INT | length |
INT * | trees |
INT | degree |
DREAL const * | position_weights |
Trie * | TreeMem |
INT | TreeMemPtr |
INT | TreeMemPtrMax |
bool | use_compact_terminal_nodes |
bool | weights_in_tree |
INT * | nofsKmers |
void CTrie< Trie >::destroy | ( | ) |
void CTrie< Trie >::delete_trees | ( | bool | p_use_compact_terminal_nodes = true |
) |
void 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 | |||
) |
compute by tree helper
vec | vector | |
len | length | |
seq_pos | sequence position | |
tree_pos | tree position | |
weight_pos | weight position | |
LevelContrib | level contribution | |
factor | factor | |
mkl_stepsize | MKL stepsize | |
weights | ||
degree_times_position_weights | if degree times position weights shall be applied |
void CTrie< Trie >::fill_backtracking_table_recursion | ( | Trie * | tree, | |
INT | depth, | |||
ULONG | seq, | |||
DREAL | value, | |||
CDynamicArray< ConsensusEntry > * | table, | |||
DREAL * | weights | |||
) |
void CTrie< Trie >::fill_backtracking_table | ( | INT | pos, | |
CDynamicArray< ConsensusEntry > * | prev, | |||
CDynamicArray< ConsensusEntry > * | cur, | |||
bool | cumulative, | |||
DREAL * | weights | |||
) |
POIMs extract W
W | W | |
K | K |
POIMs precalc SLR
distrib | distribution |
void CTrie< Trie >::POIMs_get_SLR | ( | const INT | parentIdx, | |
const INT | sym, | |||
const int | depth, | |||
DREAL * | S, | |||
DREAL * | L, | |||
DREAL * | R | |||
) |
POIMs get SLR
parentIdx | parent index | |
sym | symbol | |
depth | depth | |
S | will point to S | |
L | will point to L | |
R | will point to R |
void CTrie< Trie >::POIMs_add_SLR | ( | DREAL *const *const | poims, | |
const INT | K, | |||
const INT | debug | |||
) |
POIMs add SLR
poims | POIMs | |
K | K | |
debug | debug level |
bool CTrie< Trie >::get_use_compact_terminal_nodes | ( | ) |
void CTrie< Trie >::set_use_compact_terminal_nodes | ( | bool | p_use_compact_terminal_nodes | ) |
void CTrie< Trie >::check_treemem | ( | ) |
void CTrie< Trie >::set_weights_in_tree | ( | bool | weights_in_tree_ | ) |
bool CTrie< Trie >::get_weights_in_tree | ( | ) |
void 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 | |||
) |
POIMs extract W helper
nodeIdx | node index | |
depth | depth | |
offset | offset | |
y0 | y0 | |
W | W | |
K | K |
void 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 | |||
) |
POIMs calc SLR helper
distrib | distribution | |
i | i | |
nodeIdx | node index | |
left_tries_idx | left tries index | |
depth | depth | |
lastSym | last symbol | |
S | S | |
L | L | |
R | R |
void 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 | |||
) |
POIMs calc SLR helper 2
distrib | distribution | |
i | i | |
nodeIdx | node index | |
left_tries_idx | left tries index | |
depth | depth | |
S | S | |
L | L | |
R | R |
void 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 | |||
) |
POIMs add SLR helper 1
nodeIdx | node index | |
depth | depth | |
i | i | |
y0 | y0 | |
poims | POIMs | |
K | K | |
debug | debug level |
void 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 | |||
) |
POIMs add SLR helper 2
poims | POIMs | |
K | K | |
k | k | |
i | i | |
y | y | |
valW | value W | |
valS | value S | |
valL | value L | |
valR | value R | |
debug | debug level |
DREAL const* CTrie< Trie >::position_weights [protected] |
INT CTrie< Trie >::TreeMemPtr [protected] |
INT CTrie< Trie >::TreeMemPtrMax [protected] |
bool CTrie< Trie >::use_compact_terminal_nodes [protected] |
bool CTrie< Trie >::weights_in_tree [protected] |
CParallel CSGObject::parallel [static, inherited] |
Definition at line 105 of file SGObject.h.
CIO CSGObject::io [static, inherited] |
Definition at line 106 of file SGObject.h.
CVersion CSGObject::version [static, inherited] |
Definition at line 107 of file SGObject.h.