RNAlib-2.2.0-RC3

The most basic data structure required by many functions throughout the RNAlib. More...

+ Collaboration diagram for vrna_fold_compound:

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_thc
 The hard constraints data structure used for structure prediction.
 
vrna_mx_mfe_tmatrices
 The MFE DP matrices.
 
vrna_mx_pf_texp_matrices
 The PF DP matrices.
 
struct vrna_param_tparams
 The precomputed free energy contributions for each type of loop.
 
struct vrna_exp_param_texp_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_tsc
 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.
 

Detailed Description

The most basic data structure required by many functions throughout the RNAlib.

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!
See also
vrna_fold_compound.type, vrna_get_fold_compound(), vrna_get_fold_compound_ali(), vrna_free_fold_compound(), VRNA_VC_TYPE_SINGLE, VRNA_VC_TYPE_ALIGNMENT

Field Documentation

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

Warning
Do not edit this attribute, it will be automagically set by the corresponding get() methods for the vrna_fold_compound. The value specified in this attribute dictates the set of other attributes to use within this data structure.
char* vrna_fold_compound::sequence

The input sequence string.

Warning
Only available if
type==VRNA_VC_TYPE_SINGLE 
short* vrna_fold_compound::sequence_encoding

Numerical encoding of the input sequence.

See also
vrna_sequence_encode()
Warning
Only available if
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.

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_VC_TYPE_SINGLE 
See also
vrna_get_indx(), vrna_get_ptypes()
char* vrna_fold_compound::ptype_pf_compat

ptype array indexed via iindx

Deprecated:
This attribute will vanish in the future! It's meant for backward compatibility only!
Warning
Only available if
type==VRNA_VC_TYPE_SINGLE 
struct vrna_sc_t* vrna_fold_compound::sc

The soft constraints for usage in structure prediction and evaluation.

Warning
Only available if
type==VRNA_VC_TYPE_SINGLE 
char** vrna_fold_compound::sequences

The aligned sequences.

Note
The end of the alignment is indicated by a NULL pointer in the second dimension
Warning
Only available if
type==VRNA_VC_TYPE_ALIGNMENT 
unsigned int vrna_fold_compound::n_seq

The number of sequences in the alignment.

Warning
Only available if
type==VRNA_VC_TYPE_ALIGNMENT 
char* vrna_fold_compound::cons_seq

The consensus sequence of the aligned sequences.

Warning
Only available if
type==VRNA_VC_TYPE_ALIGNMENT 
short* vrna_fold_compound::S_cons

Numerical encoding of the consensus sequence.

Warning
Only available if
type==VRNA_VC_TYPE_ALIGNMENT 
short** vrna_fold_compound::S

Numerical encoding of the sequences in the alignment.

Warning
Only available if
type==VRNA_VC_TYPE_ALIGNMENT 
short** vrna_fold_compound::S5

S5[s][i] holds next base 5' of i in sequence s.

Warning
Only available if
type==VRNA_VC_TYPE_ALIGNMENT 
short** vrna_fold_compound::S3

Sl[s][i] holds next base 3' of i in sequence s.

Warning
Only available if
type==VRNA_VC_TYPE_ALIGNMENT 
int* vrna_fold_compound::pscore

Precomputed array of pair types expressed as pairing scores.

Warning
Only available if
type==VRNA_VC_TYPE_ALIGNMENT 
struct vrna_sc_t** vrna_fold_compound::scs

A set of soft constraints (for each sequence in the alignment)

Warning
Only available if
type==VRNA_VC_TYPE_ALIGNMENT 

The documentation for this struct was generated from the following file: