This module provides interfaces that deal with creation and destruction of dynamic programming matrices used within the RNAlib. More…
// typedefs typedef struct vrna_mx_mfe_s vrna_mx_mfe_t typedef struct vrna_mx_pf_s vrna_mx_pf_t // enums enum vrna_mx_type_e // structs struct vrna_mx_mfe_s struct vrna_mx_pf_s // global functions int vrna_mx_add ( vrna_fold_compound_t* vc, vrna_mx_type_e type, unsigned int options ) int vrna_mx_mfe_add ( vrna_fold_compound_t* vc, vrna_mx_type_e mx_type, unsigned int options ) int vrna_mx_pf_add ( vrna_fold_compound_t* vc, vrna_mx_type_e mx_type, unsigned int options ) int vrna_mx_prepare ( vrna_fold_compound_t* vc, unsigned int options ) void vrna_mx_mfe_free (vrna_fold_compound_t* vc) void vrna_mx_pf_free (vrna_fold_compound_t* vc)
typedef struct vrna_mx_mfe_s vrna_mx_mfe_t
typedef struct vrna_mx_pf_s vrna_mx_pf_t
int vrna_mx_add ( vrna_fold_compound_t* vc, vrna_mx_type_e type, unsigned int options )
This function adds DP matrices of a specific type to the provided vrna_fold_compound_t , such that successive DP recursion can be applied. The function caller has to specify which type of DP matrix is requested, see vrna_mx_type_e , and what kind of recursive algorithm will be applied later on, using the parameters type, and options, respectively. For the latter, Minimum free energy (MFE), and Partition function (PF) computations are distinguished. A third option that may be passed is VRNA_OPTION_HYBRID , indicating that auxiliary DP arrays are required for RNA-RNA interaction prediction.
Parameters:
vc | The vrna_fold_compound_t that holds pointers to the DP matrices |
type | The type of DP matrices requested |
options | Option flags that specify the kind of DP matrices, such as MFE or PF arrays, and auxiliary requirements |
Returns:
1 if DP matrices were properly allocated and attached, 0 otherwise
Note
Usually, there is no need to call this function, since the constructors of vrna_fold_compound_t are handling all the DP matrix memory allocation.
void vrna_mx_mfe_free (vrna_fold_compound_t* vc)
Parameters:
vc | The vrna_fold_compound_t storing the MFE DP matrices that are to be erased from memory |
void vrna_mx_pf_free (vrna_fold_compound_t* vc)
Parameters:
vc | The vrna_fold_compound_t storing the PF DP matrices that are to be erased from memory |