RNAlib-2.2.7
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Go to the source code of this file.
Data Structures | |
struct | vrna_basepair_s |
Base pair data structure used in subopt.c. More... | |
struct | vrna_plist_s |
this datastructure is used as input parameter in functions of PS_dot.h and others More... | |
struct | vrna_cpair_s |
this datastructure is used as input parameter in functions of PS_dot.c More... | |
struct | vrna_sect_s |
Stack of partial structures for backtracking. More... | |
struct | vrna_bp_stack_s |
Base pair stack element. More... | |
struct | pu_contrib |
contributions to p_u More... | |
struct | interact |
struct | pu_out |
Collection of all free_energy of beeing unpaired values for output. More... | |
struct | constrain |
constraints for cofolding More... | |
struct | duplexT |
struct | node |
struct | snoopT |
struct | dupVar |
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_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_EVAL_ONLY 8U |
Option flag to specify that neither MFE, nor PF DP matrices are required. More... | |
Typedefs | |
typedef struct vrna_fc_s | vrna_fold_compound_t |
Typename for the fold_compound data structure vrna_fc_s. | |
typedef struct vrna_basepair_s | vrna_basepair_t |
Typename for the base pair repesenting data structure vrna_basepair_s. | |
typedef struct vrna_plist_s | vrna_plist_t |
Typename for the base pair list repesenting data structure vrna_plist_s. | |
typedef struct vrna_bp_stack_s | vrna_bp_stack_t |
Typename for the base pair stack repesenting data structure vrna_bp_stack_s. | |
typedef struct vrna_cpair_s | vrna_cpair_t |
Typename for data structure vrna_cpair_s. | |
typedef struct vrna_sect_s | vrna_sect_t |
Typename for stack of partial structures vrna_sect_s. | |
typedef double | FLT_OR_DBL |
Typename for floating point number in partition function computations. | |
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... | |
typedef struct vrna_basepair_s | PAIR |
Old typename of vrna_basepair_s. More... | |
typedef struct vrna_plist_s | plist |
Old typename of vrna_plist_s. More... | |
typedef struct vrna_cpair_s | cpair |
Old typename of vrna_cpair_s. More... | |
typedef struct vrna_sect_s | sect |
Old typename of vrna_sect_s. More... | |
typedef struct vrna_bp_stack_s | bondT |
Old typename of vrna_bp_stack_s. More... | |
typedef struct pu_contrib | pu_contrib |
contributions to p_u | |
typedef struct pu_out | pu_out |
Collection of all free_energy of beeing unpaired values for output. | |
typedef struct constrain | constrain |
constraints for cofolding | |
Enumerations | |
enum | vrna_fc_type_e { VRNA_VC_TYPE_SINGLE, VRNA_VC_TYPE_ALIGNMENT } |
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, 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 *vc) |
Free memory occupied by a vrna_fold_compound_t. More... | |
void | vrna_fold_compound_add_auxdata (vrna_fold_compound_t *vc, 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 *vc, vrna_callback_recursion_status *f) |
Add a recursion status callback to the vrna_fold_compound_t. More... | |