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RNAlib-2.4.17
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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. More... | |
| #define | VRNA_STATUS_MFE_POST (unsigned char)2 |
| Status message indicating that MFE computations are finished. More... | |
| #define | VRNA_STATUS_PF_PRE (unsigned char)3 |
| Status message indicating that Partition function computations are about to begin. More... | |
| #define | VRNA_STATUS_PF_POST (unsigned char)4 |
| Status message indicating that Partition function computations are finished. More... | |
| #define | VRNA_OPTION_DEFAULT 0U |
| Option flag to specify default settings/requirements. | |
| #define | VRNA_OPTION_MFE 1U |
| Option flag to specify requirement of Minimum Free Energy (MFE) DP matrices and corresponding set of energy parameters. More... | |
| #define | VRNA_OPTION_PF 2U |
| Option flag to specify requirement of Partition Function (PF) DP matrices and corresponding set of Boltzmann factors. More... | |
| #define | VRNA_OPTION_HYBRID 4U |
| Option flag to specify requirement of dimer DP matrices. | |
| #define | VRNA_OPTION_EVAL_ONLY 8U |
| Option flag to specify that neither MFE, nor PF DP matrices are required. More... | |
| #define | VRNA_OPTION_WINDOW 16U |
| 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_callback_free_auxdata(void *data) |
| Callback to free memory allocated for auxiliary user-provided data. More... | |
| typedef void() | vrna_callback_recursion_status(unsigned char status, void *data) |
| Callback to perform specific user-defined actions before, or after recursive computations. More... | |
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. More... | |
| 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. More... | |
| void | vrna_fold_compound_free (vrna_fold_compound_t *fc) |
| Free memory occupied by a vrna_fold_compound_t. More... | |
| void | vrna_fold_compound_add_auxdata (vrna_fold_compound_t *fc, void *data, vrna_callback_free_auxdata *f) |
| Add auxiliary data to the vrna_fold_compound_t. More... | |
| void | vrna_fold_compound_add_callback (vrna_fold_compound_t *fc, vrna_callback_recursion_status *f) |
| Add a recursion status callback to the vrna_fold_compound_t. More... | |
The Basic Fold Compound API.