RNAlib-2.6.3
 
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fold_compound.h File Reference

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_tvrna_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_tvrna_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.