1 #ifndef VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 2 #define VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H 71 #define VRNA_STATUS_MFE_PRE (unsigned char)1 80 #define VRNA_STATUS_MFE_POST (unsigned char)2 88 #define VRNA_STATUS_PF_PRE (unsigned char)3 96 #define VRNA_STATUS_PF_POST (unsigned char)4 100 #define VRNA_BACKWARD_COMPAT 103 #ifdef VRNA_BACKWARD_COMPAT 265 double energy_backtrack;
266 double opening_backtrack_x;
267 double opening_backtrack_y;
312 float fullStemEnergy;
441 #if __STDC_VERSION__ >= 201112L 458 short *sequence_encoding2;
481 #if __STDC_VERSION__ >= 201112L 514 unsigned short **a2s;
526 #if __STDC_VERSION__ >= 201112L 576 #define VRNA_OPTION_MFE 1 584 #define VRNA_OPTION_PF 2 586 #define VRNA_OPTION_HYBRID 4 597 #define VRNA_OPTION_EVAL_ONLY 8 599 #define VRNA_OPTION_WINDOW 16 635 unsigned int options);
668 unsigned int options);
671 vrna_fold_compound_TwoD(
const char *sequence,
675 unsigned int options);
short ** S3
Sl[s][i] holds next base 3' of i in sequence s.
Definition: data_structures.h:510
short ** S
Numerical encoding of the sequences in the alignment.
Definition: data_structures.h:504
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.
int l
j<l in shorter seq
Definition: data_structures.h:227
double ** M
multi loops
Definition: data_structures.h:209
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition: data_structures.h:546
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_f...
Definition: dp_matrices.h:39
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.
short * S_cons
Numerical encoding of the consensus sequence.
Definition: data_structures.h:501
char * ptype
Pair type array.
Definition: data_structures.h:459
short * sequence_encoding
Numerical encoding of the input sequence.
Definition: data_structures.h:454
double ** H
hairpin loops
Definition: data_structures.h:207
vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors.
Definition: data_structures.h:413
struct constrain constrain
constraints for cofolding
int u_vals
number of different -u values
Definition: data_structures.h:236
Definition: data_structures.h:325
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j].
Definition: data_structures.h:544
short * reference_pt1
A pairtable of the first reference structure.
Definition: data_structures.h:539
vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition: data_structures.h:473
struct pu_contrib pu_contrib
contributions to p_u
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:389
char ** sequences
The aligned sequences.
Definition: data_structures.h:491
int j
j<l in shorter seq
Definition: data_structures.h:226
Definition: data_structures.h:287
contributions to p_u
Definition: data_structures.h:206
int contribs
[-c "SHIME"]
Definition: data_structures.h:237
The model details data structure and its corresponding modifiers.
void * auxdata
A pointer to auxiliary, user-defined data.
Definition: data_structures.h:429
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
int i
k<i in longer seq
Definition: data_structures.h:224
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.
Definition: data_structures.h:296
double ** u_values
(the -u values * [-c "SHIME"]) * seq len
Definition: data_structures.h:239
char * cons_seq
The consensus sequence of the aligned sequences.
Definition: data_structures.h:498
vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition: data_structures.h:407
char * ptype_pf_compat
ptype array indexed via iindx
Definition: data_structures.h:468
Definition: data_structures.h:372
Stack of partial structures for backtracking.
Definition: data_structures.h:182
this datastructure is used as input parameter in functions of PS_dot.c
Definition: data_structures.h:173
int * jindx
DP matrix accessor.
Definition: data_structures.h:416
void vrna_fold_compound_free(vrna_fold_compound_t *vc)
Free memory occupied by a vrna_fold_compound_t.
vrna_fc_type_e
An enumerator that is used to specify the type of a vrna_fold_compound_t.
Definition: data_structures.h:371
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...
Base pair data structure used in subopt.c.
Definition: data_structures.h:155
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:187
The soft constraints data structure.
Definition: constraints.h:511
int w
longest unpaired region
Definition: data_structures.h:212
struct pu_out pu_out
Collection of all free_energy of beeing unpaired values for output.
short ** S5
S5[s][i] holds next base 5' of i in sequence s.
Definition: data_structures.h:507
void( vrna_callback_recursion_status)(vrna_fold_compound_t *vc, unsigned char status)
Callback to perform specific user-defined actions before, or after recursive computations.
Definition: data_structures.h:61
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
vrna_sc_t ** scs
A set of soft constraints (for each sequence in the alignment)
Definition: data_structures.h:518
void( vrna_callback_free_auxdata)(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: data_structures.h:51
int k
k<i in longer seq
Definition: data_structures.h:225
The hard constraints data structure.
Definition: constraints.h:468
Definition: data_structures.h:218
double * Pi
probabilities of interaction
Definition: data_structures.h:219
int oldAliEn
use old alifold energies (with gaps)
constraints for cofolding
Definition: data_structures.h:245
double ** I
interior loops
Definition: data_structures.h:208
int len
sequence length
Definition: data_structures.h:235
int length
length of the input sequence
Definition: data_structures.h:211
char ** header
header line
Definition: data_structures.h:238
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:163
vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition: data_structures.h:412
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition: data_structures.h:515
unsigned int n_seq
The number of sequences in the alignment.
Definition: data_structures.h:495
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition: data_structures.h:543
int length
length of longer sequence
Definition: data_structures.h:228
char * sequence
The input sequence string.
Definition: data_structures.h:451
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition: data_structures.h:409
Definition: data_structures.h:373
vrna_callback_recursion_status * stat_cb
Recursion status callback (usually called just before, and after recursive computations in the librar...
Definition: data_structures.h:424
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint...
Definition: data_structures.h:403
vrna_callback_free_auxdata * free_auxdata
A callback to free auxiliary user data whenever the fold_compound itself is free'd.
Definition: data_structures.h:433
Collection of all free_energy of beeing unpaired values for output.
Definition: data_structures.h:234
double Gikjl
full free energy for interaction between [k,i] k<i in longer seq and [j,l] j<l in shorter seq ...
Definition: data_structures.h:221
unsigned int length
The length of the sequence (or sequence alignment)
Definition: data_structures.h:402
Base pair stack element.
Definition: data_structures.h:191
double * Gi
free energies of interaction
Definition: data_structures.h:220
short * reference_pt2
A pairtable of the second reference structure.
Definition: data_structures.h:540
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition: data_structures.h:537
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition: data_structures.h:547
Definition: data_structures.h:259
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition: data_structures.h:542
vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition: data_structures.h:395
int window_size
window size for local folding sliding window approach
Definition: data_structures.h:559
char ** ptype_local
Pair type array (for local folding)
Definition: data_structures.h:560
double Gikjl_wo
Gikjl without contributions for prob_unpaired.
Definition: data_structures.h:223
int * iindx
DP matrix accessor.
Definition: data_structures.h:415
double ** E
exterior loop
Definition: data_structures.h:210
Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fol...
Definition: dp_matrices.h:197
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition: data_structures.h:538
vrna_mx_pf_t * exp_matrices
The PF DP matrices.
Definition: data_structures.h:410