The Basic Fold Compound API. More...

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Data Structures
struct	vrna_fc_s
	The most basic data structure required by many functions throughout the RNAlib. More...

Macros
#define	VRNA_STATUS_MFE_PRE (unsigned char)1
	Status message indicating that MFE computations are about to begin.

#define	VRNA_STATUS_MFE_POST (unsigned char)2
	Status message indicating that MFE computations are finished.

#define	VRNA_STATUS_PF_PRE (unsigned char)3
	Status message indicating that Partition function computations are about to begin.

#define	VRNA_STATUS_PF_POST (unsigned char)4
	Status message indicating that Partition function computations are finished.

#define	VRNA_OPTION_DEFAULT 0U
	Option flag to specify default settings/requirements.

#define	VRNA_OPTION_MFE (1 << 0)
	Option flag to specify requirement of Minimum Free Energy (MFE) DP matrices and corresponding set of energy parameters.

#define	VRNA_OPTION_PF (1 << 1)
	Option flag to specify requirement of Partition Function (PF) DP matrices and corresponding set of Boltzmann factors.

#define	VRNA_OPTION_HYBRID (1 << 2)
	Option flag to specify requirement of dimer DP matrices.

#define	VRNA_OPTION_EVAL_ONLY (1 << 3)
	Option flag to specify that neither MFE, nor PF DP matrices are required.

#define	VRNA_OPTION_WINDOW (1 << 4)
	Option flag to specify requirement of DP matrices for local folding approaches.

Typedefs
typedef struct vrna_fc_s	vrna_fold_compound_t
	Typename for the fold_compound data structure vrna_fc_s.

typedef void(*	vrna_auxdata_free_f) (void *data)
	Callback to free memory allocated for auxiliary user-provided data.

typedef void()	vrna_callback_free_auxdata(void *data)
	Callback to free memory allocated for auxiliary user-provided data.

typedef void(*	vrna_recursion_status_f) (unsigned char status, void *data)
	Callback to perform specific user-defined actions before, or after recursive computations.

Enumerations
enum	vrna_fc_type_e { VRNA_FC_TYPE_SINGLE , VRNA_FC_TYPE_COMPARATIVE }
	An enumerator that is used to specify the type of a vrna_fold_compound_t. More...

Functions
vrna_fold_compound_t *	vrna_fold_compound (const char sequence, const vrna_md_t md_p, unsigned int options)
	Retrieve a vrna_fold_compound_t data structure for single sequences and hybridizing sequences.

vrna_fold_compound_t *	vrna_fold_compound_comparative (const char *sequences, vrna_md_t md_p, unsigned int options)
	Retrieve a vrna_fold_compound_t data structure for sequence alignments.

void	vrna_fold_compound_free (vrna_fold_compound_t *fc)
	Free memory occupied by a vrna_fold_compound_t.

void	vrna_fold_compound_add_auxdata (vrna_fold_compound_t fc, void data, vrna_auxdata_free_f f)
	Add auxiliary data to the vrna_fold_compound_t.

void	vrna_fold_compound_add_callback (vrna_fold_compound_t *fc, vrna_recursion_status_f f)
	Add a recursion status callback to the vrna_fold_compound_t.

Detailed Description

The Basic Fold Compound API.

Data Structures