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RNAlib-2.2.10
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Include dependency graph for data_structures.h:
This graph shows which files directly or indirectly include this file: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 |
| interaction data structure for RNAup More... | |
| struct | pu_out |
| Collection of all free_energy of beeing unpaired values for output. More... | |
| struct | constrain |
| constraints for cofolding More... | |
| struct | duplexT |
| Data structure for RNAduplex. More... | |
| struct | node |
| Data structure for RNAsnoop (fold energy list) More... | |
| struct | snoopT |
| Data structure for RNAsnoop. More... | |
| struct | dupVar |
| Data structure used in RNApkplex. More... | |
| 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 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 interact | interact |
| interaction data structure for RNAup | |
| typedef struct pu_out | pu_out |
| Collection of all free_energy of beeing unpaired values for output. | |
| typedef struct constrain | constrain |
| constraints for cofolding | |
| typedef struct node | folden |
| Data structure for RNAsnoop (fold energy list) | |
| typedef struct dupVar | dupVar |
| Data structure used in RNApkplex. | |
Enumerations |
Functions | |
| void | vrna_C11_features (void) |
| Dummy symbol to check whether the library was build using C11/C++11 features. More... | |
| 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... | |