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. | |
The Basic Fold Compound API.