Partition Function and Base Pair Probabilities for Sequence Alignment(s)

Collaboration diagram for Partition Function and Base Pair Probabilities for Sequence Alignment(s):

Functions
float	alipf_fold_par (const char **sequences, char *structure, plist **pl, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)
float	alipf_fold (const char **sequences, char *structure, plist **pl)
	The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of pair_info structs. The list is terminated by the first entry with pi.i = 0.
float	alipf_circ_fold (const char **sequences, char *structure, plist **pl)
double *	export_ali_bppm (void)
	Get a pointer to the base pair probability array.

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Detailed Description

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Function Documentation

float alipf_fold_par	(	const char **	sequences,
		char *	structure,
		plist **	pl,
		pf_paramT *	parameters,
		int	calculate_bppm,
		int	is_constrained,
		int	is_circular
	)

Parameters:

sequences
structure
pl
parameters
calculate_bppm
is_constrained
is_circular

Returns:

float alipf_fold	(	const char **	sequences,
		char *	structure,
		plist **	pl
	)

The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of pair_info structs. The list is terminated by the first entry with pi.i = 0.

Parameters:

sequences
structure
pl

Returns:

float alipf_circ_fold	(	const char **	sequences,
		char *	structure,
		plist **	pl
	)

Parameters:

sequences
structure
pl

Returns:

double* export_ali_bppm

(

void

)

Get a pointer to the base pair probability array.

Accessing the base pair probabilities for a pair (i,j) is achieved by

FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; 

See also:

get_iindx()

Returns:

A pointer to the base pair probability array