#include <ViennaRNA/fold_compound.h>
The most basic data structure required by many functions throughout the RNAlib. More…
// fields vrna_fc_type_e type unsigned int length int cutpoint unsigned int* strand_number unsigned int* strand_order unsigned int* strand_start unsigned int* strand_end unsigned int strands vrna_seq_t* nucleotides vrna_hc_t* hc vrna_mx_mfe_t* matrices vrna_mx_pf_t* exp_matrices vrna_param_t* params vrna_exp_param_t* exp_params int* iindx int* jindx vrna_callback_recursion_status* stat_cb void* auxdata vrna_callback_free_auxdata* free_auxdata vrna_sd_t* domains_struc vrna_ud_t* domains_up vrna_gr_aux_t* aux_grammar unsigned int maxD1 unsigned int maxD2 short* reference_pt1 short* reference_pt2 unsigned int* referenceBPs1 unsigned int* referenceBPs2 unsigned int* bpdist unsigned int* mm1 unsigned int* mm2 int window_size char** ptype_local char* sequence short* sequence_encoding short* sequence_encoding2 char* ptype char* ptype_pf_compat vrna_sc_t* sc char** sequences unsigned int n_seq char* cons_seq short* S_cons short** S short** S5 short** S3 char** Ss unsigned int** a2s int* pscore int** pscore_local short* pscore_pf_compat vrna_sc_t** scs int oldAliEn
SWIG Wrapper Notes This data structure is wrapped as an object fold_compound with several related functions attached as methods.
A new fold_compound can be obtained by calling one of its constructors:
The resulting object has a list of attached methods which in most cases directly correspond to functions that mainly operate on the corresponding C data structure:
Note
Please read the documentation of this data structure carefully! Some attributes are only available for specific types this data structure can adopt.
Warning
Reading/Writing from/to attributes that are not within the scope of the current type usually result in undefined behavior!
vrna_fc_type_e type
Currently possible values are VRNA_FC_TYPE_SINGLE , and VRNA_FC_TYPE_COMPARATIVE
Warning
Do not edit this attribute, it will be automagically set by the corresponding get() methods for the vrna_fold_compound_t . The value specified in this attribute dictates the set of other attributes to use within this data structure.
unsigned int length
int cutpoint
unsigned int* strand_number
vrna_hc_t* hc
vrna_mx_mfe_t* matrices
vrna_mx_pf_t* exp_matrices
vrna_param_t* params
vrna_exp_param_t* exp_params
int* iindx
int* jindx
vrna_callback_recursion_status* stat_cb
void* auxdata
vrna_callback_free_auxdata* free_auxdata
vrna_sd_t* domains_struc
vrna_ud_t* domains_up
unsigned int maxD1
unsigned int maxD2
short* reference_pt1
short* reference_pt2
unsigned int* referenceBPs1
unsigned int* referenceBPs2
unsigned int* bpdist
unsigned int* mm1
unsigned int* mm2
int window_size
char** ptype_local
char* sequence
Warning
Only available if
type==VRNA_FC_TYPE_SINGLE
short* sequence_encoding
Warning
Only available if
type==VRNA_FC_TYPE_SINGLE
See also:
vrna_sequence_encode()
char* ptype
Contains the numerical encoding of the pair type for each pair (i,j) used in MFE, Partition function and Evaluation computations.
Note
This array is always indexed via jindx, in contrast to previously different indexing between mfe and pf variants!
Warning
Only available if
type==VRNA_FC_TYPE_SINGLE
See also:
char* ptype_pf_compat
Deprecated This attribute will vanish in the future! It’s meant for backward compatibility only!
Warning
Only available if
type==VRNA_FC_TYPE_SINGLE
vrna_sc_t* sc
Warning
Only available if
type==VRNA_FC_TYPE_SINGLE
char** sequences
Note
The end of the alignment is indicated by a NULL pointer in the second dimension
Warning
Only available if
type==VRNA_FC_TYPE_COMPARATIVE
unsigned int n_seq
Warning
Only available if
type==VRNA_FC_TYPE_COMPARATIVE
char* cons_seq
Warning
Only available if
type==VRNA_FC_TYPE_COMPARATIVE
short* S_cons
Warning
Only available if
type==VRNA_FC_TYPE_COMPARATIVE
short** S
Warning
Only available if
type==VRNA_FC_TYPE_COMPARATIVE
short** S5
Warning
Only available if
type==VRNA_FC_TYPE_COMPARATIVE
short** S3
Warning
Only available if
type==VRNA_FC_TYPE_COMPARATIVE
int* pscore
Warning
Only available if
type==VRNA_FC_TYPE_COMPARATIVE
int** pscore_local
Warning
Only available if
type==VRNA_FC_TYPE_COMPARATIVE
short* pscore_pf_compat
Deprecated This attribute will vanish in the future!
Warning
Only available if
type==VRNA_FC_TYPE_COMPARATIVE
vrna_sc_t** scs
Warning
Only available if
type==VRNA_FC_TYPE_COMPARATIVE