Scanning version using a sliding window approach to compute equilibrium probabilities. More...

Detailed Description

Scanning version using a sliding window approach to compute equilibrium probabilities.

Collaboration diagram for Local (sliding window) Partition Function and Equilibrium Probabilities:

Modules
	Deprecated Interface for Local (Sliding Window) Partition Function Computation

Files
file	part_func_window.h
	Partition function and equilibrium probability implementation for the sliding window algorithm.

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...

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...

Macro Definition Documentation

#define VRNA_PROBS_WINDOW_BPP 4096U

#include <ViennaRNA/part_func_window.h>

Trigger base pairing probabilities.

Passing this flag to vrna_probs_window() activates callback execution for base pairing probabilities. In turn, the corresponding callback receives this flag through the type argument whenever base pairing probabilities are provided.

Detailed information for the algorithm to compute unpaired probabilities can be taken from [1].

See also: vrna_probs_window()

#define VRNA_PROBS_WINDOW_UP 8192U

#include <ViennaRNA/part_func_window.h>

Trigger unpaired probabilities.

Passing this flag to vrna_probs_window() activates callback execution for unpaired probabilities. In turn, the corresponding callback receives this flag through the type argument whenever unpaired probabilities are provided.

Detailed information for the algorithm to compute unpaired probabilities can be taken from [4].

See also: vrna_probs_window()

#define VRNA_PROBS_WINDOW_STACKP 16384U

#include <ViennaRNA/part_func_window.h>

Trigger base pair stack probabilities.

Passing this flag to vrna_probs_window() activates callback execution for stacking probabilities. In turn, the corresponding callback receives this flag through the type argument whenever stack probabilities are provided.

Bug:: Currently, this flag is a placeholder doing nothing as the corresponding implementation for stack probability computation is missing.

See also: vrna_probs_window()

#define VRNA_PROBS_WINDOW_UP_SPLIT 32768U

#include <ViennaRNA/part_func_window.h>

Trigger detailed unpaired probabilities split up into different loop type contexts.

Passing this flag to vrna_probs_window() activates callback execution for unpaired probabilities. In contrast to VRNA_PROBS_WINDOW_UP this flag requests unpaired probabilities to be split up into different loop type contexts. In turn, the corresponding callback receives the VRNA_PROBS_WINDOW_UP flag OR-ed together with the corresponding loop type, i.e.:

VRNA_EXT_LOOP - Exterior loop.
VRNA_HP_LOOP - Hairpin loop.
VRNA_INT_LOOP - Internal loop.
VRNA_MB_LOOP - Multibranch loop.
VRNA_ANY_LOOP - Any loop.

See also: vrna_probs_window(), VRNA_PROBS_WINDOW_UP

#define VRNA_PROBS_WINDOW_PF 65536U

#include <ViennaRNA/part_func_window.h>

Trigger partition function.

Passing this flag to vrna_probs_window() activates callback execution for partition function. In turn, the corresponding callback receives this flag through it's type argument whenever partition function data is provided.

Note: Instead of actually providing the partition function , the callback is always provided with the corresponding enemble free energy $\Delta G = - RT \ln Z$ .

See also: vrna_probs_window()

Typedef Documentation

typedef void( vrna_probs_window_callback) (FLT_OR_DBL *pr, int pr_size, int i, int max, unsigned int type, void *data)

#include <ViennaRNA/part_func_window.h>

Sliding window probability computation callback.

Notes on Callback Functions:: This function will be called for each probability data set in the sliding window probability computation implementation of vrna_probs_window(). The argument type specifies the type of probability that is passed to this function.

Types:

VRNA_PROBS_WINDOW_BPP - Trigger base pairing probabilities.
VRNA_PROBS_WINDOW_UP - Trigger unpaired probabilities.
VRNA_PROBS_WINDOW_PF - Trigger partition function.

The above types usually come exclusively. However, for unpaired probabilities, the VRNA_PROBS_WINDOW_UP flag is OR-ed together with one of the loop type contexts

VRNA_EXT_LOOP - Exterior loop.
VRNA_HP_LOOP - Hairpin loop.
VRNA_INT_LOOP - Internal loop.
VRNA_MB_LOOP - Multibranch loop.
VRNA_ANY_LOOP - Any loop.

to indicate the particular type of data available through the pr pointer.

See also: vrna_probs_window(), vrna_pfl_fold_up_cb()

Parameters

pr	An array of probabilities
pr_size	The length of the probability array
i	The i-position (5') of the probabilities
max	The (theoretical) maximum length of the probability array
type	The type of data that is provided
data	Auxiliary data

Function Documentation

int vrna_probs_window	(	vrna_fold_compound_t *	fc,
		int	ulength,
		unsigned int	options,
		vrna_probs_window_callback *	cb,
		void *	data
	)

#include <ViennaRNA/part_func_window.h>

Compute various equilibrium probabilities under a sliding window approach.

This function applies a sliding window scan for the sequence provided with the argument fc and reports back equilibrium probabilities through the callback function cb. The data reported to the callback depends on the options flag.

Note: The parameter ulength only affects computation and resulting data if unpaired probability computations are requested through the options flag.

Options:

VRNA_PROBS_WINDOW_BPP - Trigger base pairing probabilities.
VRNA_PROBS_WINDOW_UP - Trigger unpaired probabilities.
VRNA_PROBS_WINDOW_UP_SPLIT - Trigger detailed unpaired probabilities split up into different loop type contexts.

Options may be OR-ed together

See also: vrna_pfl_fold_cb(), vrna_pfl_fold_up_cb()

Parameters

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

Returns: 0 on failure, non-zero on success

vrna_ep_t* vrna_pfl_fold	(	const char *	sequence,
		int	window_size,
		int	max_bp_span,
		float	cutoff
	)

#include <ViennaRNA/part_func_window.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.

Note: This function uses default model settings! For custom model settings, we refer to the function vrna_probs_window().; In case of any computation errors, this function returns NULL

See also: vrna_probs_window(), vrna_pfl_fold_cb(), vrna_pfl_fold_up()

Parameters

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

Returns: A list of base pair probabilities, terminated by an entry with vrna_ep_t.i and vrna_ep_t.j set to 0

int vrna_pfl_fold_cb	(	const char *	sequence,
		int	window_size,
		int	max_bp_span,
		vrna_probs_window_callback *	cb,
		void *	data
	)

#include <ViennaRNA/part_func_window.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!

Note: This function uses default model settings! For custom model settings, we refer to the function vrna_probs_window().

See also: vrna_probs_window(), vrna_pfl_fold(), vrna_pfl_fold_up_cb()

Parameters

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`

Returns: 0 on failure, non-zero on success

double** vrna_pfl_fold_up	(	const char *	sequence,
		int	ulength,
		int	window_size,
		int	max_bp_span
	)

#include <ViennaRNA/part_func_window.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 $N \times M$ , where $N$ is the length of the sequence and $M$ 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 $X[100][5]$ .

It is the users responsibility to free the memory occupied by this matrix.

Note: This function uses default model settings! For custom model settings, we refer to the function vrna_probs_window().

Parameters

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

Returns: The probabilities to be unpaired for any segment not exceeding ulength

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
	)

#include <ViennaRNA/part_func_window.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!

Note: This function uses default model settings! For custom model settings, we refer to the function vrna_probs_window().

Parameters

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`

Returns: 0 on failure, non-zero on success

Detailed Description

Modules

Files

Macros

Typedefs

Basic local partition function interface

Simplified global partition function computation using sequence(s) or multiple sequence alignment(s)

Macro Definition Documentation

Typedef Documentation

Types:

Function Documentation

Options: