RNAlib-2.4.0
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Macros | |
#define | VRNA_PROBS_WINDOW_BPP 4096U |
Option flag to activate callback triggers for pairing probabilities. More... | |
#define | VRNA_PROBS_WINDOW_UP 8192U |
Option flag to activate callback triggers for unpaired probabilities. More... | |
#define | VRNA_PROBS_WINDOW_STACKP 16384U |
Option flag to activate callback triggers for stacking probabilities. More... | |
#define | VRNA_PROBS_WINDOW_UP_SPLIT 32768U |
Option flag to activate callback triggers for unpaired probabilities (split up into different loop types) More... | |
Functions | |
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... | |
void | 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... | |
void | 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... | |
void | 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... | |
#define VRNA_PROBS_WINDOW_BPP 4096U |
#include <ViennaRNA/LPfold.h>
Option flag to activate callback triggers for pairing probabilities.
#define VRNA_PROBS_WINDOW_UP 8192U |
#include <ViennaRNA/LPfold.h>
Option flag to activate callback triggers for unpaired probabilities.
#define VRNA_PROBS_WINDOW_STACKP 16384U |
#include <ViennaRNA/LPfold.h>
Option flag to activate callback triggers for stacking probabilities.
#define VRNA_PROBS_WINDOW_UP_SPLIT 32768U |
#include <ViennaRNA/LPfold.h>
Option flag to activate callback triggers for unpaired probabilities (split up into different loop types)
vrna_ep_t* vrna_pfl_fold | ( | const char * | sequence, |
int | window_size, | ||
int | max_bp_span, | ||
float | cutoff | ||
) |
#include <ViennaRNA/LPfold.h>
Compute base pair probabilities using a sliding-window approach.
This is a simplified wrapper to vrna_probs_window() that given a nucleid acid sequence, a window size, a maximum base pair span, and a cutoff value computes the pair probabilities for any base pair in any window. The pair probabilities are returned as a list and the user has to take care to free() the memory occupied by the list.
sequence | The nucleic acid input sequence |
window_size | The size of the sliding window |
max_bp_span | The maximum distance along the backbone between two nucleotides that form a base pairs |
cutoff | A cutoff value that omits all pairs with lower probability |
void vrna_pfl_fold_cb | ( | const char * | sequence, |
int | window_size, | ||
int | max_bp_span, | ||
vrna_probs_window_callback * | cb, | ||
void * | data | ||
) |
#include <ViennaRNA/LPfold.h>
Compute base pair probabilities using a sliding-window approach (callback version)
This is a simplified wrapper to vrna_probs_window() that given a nucleid acid sequence, a window size, a maximum base pair span, and a cutoff value computes the pair probabilities for any base pair in any window. It is similar to vrna_pfl_fold() but uses a callback mechanism to return the pair probabilities.
Read the details for vrna_probs_window() for details on the callback implementation!
sequence | The nucleic acid input sequence |
window_size | The size of the sliding window |
max_bp_span | The maximum distance along the backbone between two nucleotides that form a base pairs |
cb | The callback function which collects the pair probability data for further processing |
data | Some arbitrary data structure that is passed to the callback cb |
double** vrna_pfl_fold_up | ( | const char * | sequence, |
int | ulength, | ||
int | window_size, | ||
int | max_bp_span | ||
) |
#include <ViennaRNA/LPfold.h>
Compute probability of contiguous unpaired segments.
This is a simplified wrapper to vrna_probs_window() that given a nucleic acid sequence, a maximum length of unpaired segments (ulength
), a window size, and a maximum base pair span computes the equilibrium probability of any segment not exceeding ulength
. The probabilities to be unpaired are returned as a 1-based, 2-dimensional matrix with dimensions , where
is the length of the sequence and
is the maximum segment length. As an example, the probability of a segment of size 5 starting at position 100 is stored in the matrix entry
.
It is the users responsibility to free the memory occupied by this matrix.
sequence | The nucleic acid input sequence |
ulength | The maximal length of an unpaired segment |
window_size | The size of the sliding window |
max_bp_span | The maximum distance along the backbone between two nucleotides that form a base pairs |
ulength
void vrna_pfl_fold_up_cb | ( | const char * | sequence, |
int | ulength, | ||
int | window_size, | ||
int | max_bp_span, | ||
vrna_probs_window_callback * | cb, | ||
void * | data | ||
) |
#include <ViennaRNA/LPfold.h>
Compute probability of contiguous unpaired segments.
This is a simplified wrapper to vrna_probs_window() that given a nucleic acid sequence, a maximum length of unpaired segments (ulength
), a window size, and a maximum base pair span computes the equilibrium probability of any segment not exceeding ulength
. It is similar to vrna_pfl_fold_up() but uses a callback mechanism to return the unpaired probabilities.
Read the details for vrna_probs_window() for details on the callback implementation!
sequence | The nucleic acid input sequence |
ulength | The maximal length of an unpaired segment |
window_size | The size of the sliding window |
max_bp_span | The maximum distance along the backbone between two nucleotides that form a base pairs |
cb | The callback function which collects the pair probability data for further processing |
data | Some arbitrary data structure that is passed to the callback cb |
ulength
void vrna_probs_window | ( | vrna_fold_compound_t * | fc, |
int | ulength, | ||
unsigned int | options, | ||
vrna_probs_window_callback * | cb, | ||
void * | data | ||
) |
#include <ViennaRNA/LPfold.h>
Compute various equilibrium probabilities under a sliding window approach.
fc | The fold compound with sequence data, model settings and precomputed energy parameters |
ulength | The maximal length of an unpaired segment (only for unpaired probability computations) |
cb | The callback function which collects the pair probability data for further processing |
data | Some arbitrary data structure that is passed to the callback cb |
options | Option flags to control the behavior of this function |