Partition function and equilibrium probability implementation for the sliding window algorithm. More...
Include dependency graph for part_func_window.h: This graph shows which files directly or indirectly include this file:Go to the source code of this file.
Macros | |
| #define | VRNA_EXT_LOOP 1U |
| Exterior loop. | |
| #define | VRNA_HP_LOOP 2U |
| Hairpin loop. | |
| #define | VRNA_INT_LOOP 4U |
| Internal loop. | |
| #define | VRNA_MB_LOOP 8U |
| Multibranch loop. | |
| #define | VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP) |
| Any loop. | |
| #define | VRNA_PROBS_WINDOW_BPP 4096U |
| Trigger base pairing probabilities. More... | |
| #define | VRNA_PROBS_WINDOW_UP 8192U |
| Trigger unpaired probabilities. More... | |
| #define | VRNA_PROBS_WINDOW_STACKP 16384U |
| Trigger base pair stack probabilities. More... | |
| #define | VRNA_PROBS_WINDOW_UP_SPLIT 32768U |
| Trigger detailed unpaired probabilities split up into different loop type contexts. More... | |
| #define | VRNA_PROBS_WINDOW_PF 65536U |
| Trigger partition function. More... | |
Typedefs | |
| typedef void( | vrna_probs_window_callback) (FLT_OR_DBL *pr, int pr_size, int i, int max, unsigned int type, void *data) |
| Sliding window probability computation callback. More... | |
Functions | |
Basic local partition function interface | |
| int | vrna_probs_window (vrna_fold_compound_t *fc, int ulength, unsigned int options, vrna_probs_window_callback *cb, void *data) |
| Compute various equilibrium probabilities under a sliding window approach. More... | |
Simplified global partition function computation using sequence(s) or multiple sequence alignment(s) | |
| vrna_ep_t * | vrna_pfl_fold (const char *sequence, int window_size, int max_bp_span, float cutoff) |
| Compute base pair probabilities using a sliding-window approach. More... | |
| int | vrna_pfl_fold_cb (const char *sequence, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data) |
| Compute base pair probabilities using a sliding-window approach (callback version) More... | |
| double ** | vrna_pfl_fold_up (const char *sequence, int ulength, int window_size, int max_bp_span) |
| Compute probability of contiguous unpaired segments. More... | |
| int | vrna_pfl_fold_up_cb (const char *sequence, int ulength, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data) |
| Compute probability of contiguous unpaired segments. More... | |
Detailed Description
Partition function and equilibrium probability implementation for the sliding window algorithm.
, This file contains the implementation for sliding window partition function and equilibrium probabilities. It also provides the unpaired probability implementation from Bernhart et al. 2011 [4]
