RNAlib-2.2.0-RC3
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The most basic data structure required by many functions throughout the RNAlib. More...
Data Fields | |
Common data fields | |
vrna_vc_t | type |
The type of the vrna_fold_compound. More... | |
unsigned int | length |
The length of the sequence (or sequence alignment) | |
int | cutpoint |
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint, this field will be set to -1. | |
struct vrna_hc_t * | hc |
The hard constraints data structure used for structure prediction. | |
vrna_mx_mfe_t * | matrices |
The MFE DP matrices. | |
vrna_mx_pf_t * | exp_matrices |
The PF DP matrices. | |
struct vrna_param_t * | params |
The precomputed free energy contributions for each type of loop. | |
struct vrna_exp_param_t * | exp_params |
The precomputed free energy contributions as Boltzmann factors. | |
int * | iindx |
DP matrix accessor. | |
int * | jindx |
DP matrix accessor. | |
Data fields available for single/hybrid structure prediction | |
char * | sequence |
The input sequence string. More... | |
short * | sequence_encoding |
Numerical encoding of the input sequence. More... | |
short * | sequence_encoding2 |
char * | ptype |
Pair type array. More... | |
char * | ptype_pf_compat |
ptype array indexed via iindx More... | |
struct vrna_sc_t * | sc |
The soft constraints for usage in structure prediction and evaluation. More... | |
Data fields for consensus structure prediction | |
char ** | sequences |
The aligned sequences. More... | |
unsigned int | n_seq |
The number of sequences in the alignment. More... | |
char * | cons_seq |
The consensus sequence of the aligned sequences. More... | |
short * | S_cons |
Numerical encoding of the consensus sequence. More... | |
short ** | S |
Numerical encoding of the sequences in the alignment. More... | |
short ** | S5 |
S5[s][i] holds next base 5' of i in sequence s. More... | |
short ** | S3 |
Sl[s][i] holds next base 3' of i in sequence s. More... | |
char ** | Ss |
unsigned short ** | a2s |
int * | pscore |
Precomputed array of pair types expressed as pairing scores. More... | |
struct vrna_sc_t ** | scs |
A set of soft constraints (for each sequence in the alignment) More... | |
int | oldAliEn |
Additional data fields for Distance Class Partitioning | |
These data fields are typically populated with meaningful data only if used in the context of Distance Class Partitioning | |
unsigned int | maxD1 |
Maximum allowed base pair distance to first reference. | |
unsigned int | maxD2 |
Maximum allowed base pair distance to second reference. | |
short * | reference_pt1 |
A pairtable of the first reference structure. | |
short * | reference_pt2 |
A pairtable of the second reference structure. | |
unsigned int * | referenceBPs1 |
Matrix containing number of basepairs of reference structure1 in interval [i,j]. | |
unsigned int * | referenceBPs2 |
Matrix containing number of basepairs of reference structure2 in interval [i,j]. | |
unsigned int * | bpdist |
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j]. | |
unsigned int * | mm1 |
Maximum matching matrix, reference struct 1 disallowed. | |
unsigned int * | mm2 |
Maximum matching matrix, reference struct 2 disallowed. | |
The most basic data structure required by many functions throughout the RNAlib.
vrna_vc_t vrna_fold_compound::type |
The type of the vrna_fold_compound.
Currently possible values are VRNA_VC_TYPE_SINGLE, and VRNA_VC_TYPE_ALIGNMENT
char* vrna_fold_compound::sequence |
The input sequence string.
type==VRNA_VC_TYPE_SINGLE
short* vrna_fold_compound::sequence_encoding |
Numerical encoding of the input sequence.
type==VRNA_VC_TYPE_SINGLE
char* vrna_fold_compound::ptype |
Pair type array.
Contains the numerical encoding of the pair type for each pair (i,j) used in MFE, Partition function and Evaluation computations.
type==VRNA_VC_TYPE_SINGLE
char* vrna_fold_compound::ptype_pf_compat |
ptype array indexed via iindx
type==VRNA_VC_TYPE_SINGLE
struct vrna_sc_t* vrna_fold_compound::sc |
The soft constraints for usage in structure prediction and evaluation.
type==VRNA_VC_TYPE_SINGLE
char** vrna_fold_compound::sequences |
The aligned sequences.
type==VRNA_VC_TYPE_ALIGNMENT
unsigned int vrna_fold_compound::n_seq |
The number of sequences in the alignment.
type==VRNA_VC_TYPE_ALIGNMENT
char* vrna_fold_compound::cons_seq |
The consensus sequence of the aligned sequences.
type==VRNA_VC_TYPE_ALIGNMENT
short* vrna_fold_compound::S_cons |
Numerical encoding of the consensus sequence.
type==VRNA_VC_TYPE_ALIGNMENT
short** vrna_fold_compound::S |
Numerical encoding of the sequences in the alignment.
type==VRNA_VC_TYPE_ALIGNMENT
short** vrna_fold_compound::S5 |
S5[s][i] holds next base 5' of i in sequence s.
type==VRNA_VC_TYPE_ALIGNMENT
short** vrna_fold_compound::S3 |
Sl[s][i] holds next base 3' of i in sequence s.
type==VRNA_VC_TYPE_ALIGNMENT
int* vrna_fold_compound::pscore |
Precomputed array of pair types expressed as pairing scores.
type==VRNA_VC_TYPE_ALIGNMENT
struct vrna_sc_t** vrna_fold_compound::scs |
A set of soft constraints (for each sequence in the alignment)
type==VRNA_VC_TYPE_ALIGNMENT