RNAlib-2.6.1
 
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fold_compound.h
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1#ifndef VIENNA_RNA_PACKAGE_FOLD_COMPOUND_H
2#define VIENNA_RNA_PACKAGE_FOLD_COMPOUND_H
3
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(__clang__)
6# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
7# elif defined(__GNUC__)
8# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
9# else
10# define DEPRECATED(func, msg) func
11# endif
12#else
13# define DEPRECATED(func, msg) func
14#endif
15
39
58typedef void (*vrna_auxdata_free_f)(void *data);
59
65DEPRECATED(typedef void (vrna_callback_free_auxdata)(void *data),
66 "Use vrna_auxdata_free_f instead!");
67
86typedef void (*vrna_recursion_status_f)(unsigned char status,
87 void *data);
88
89DEPRECATED(typedef void (vrna_callback_recursion_status)(unsigned char status,
90 void *data),
91 "Use vrna_recursion_status_f instead!");
92
93
100#define VRNA_STATUS_MFE_PRE (unsigned char)1
101
108#define VRNA_STATUS_MFE_POST (unsigned char)2
109
115#define VRNA_STATUS_PF_PRE (unsigned char)3
116
122#define VRNA_STATUS_PF_POST (unsigned char)4
123
124
125#include <ViennaRNA/model.h>
127#include <ViennaRNA/sequence.h>
131#include <ViennaRNA/grammar.h>
134
135#ifdef VRNA_WITH_SVM
136#include <ViennaRNA/zscore.h>
137#endif
138
139
143typedef enum {
147
148
161struct vrna_fc_s {
173 unsigned int length;
174#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
175 DEPRECATED(int cutpoint,
176 "Use strand_* members instead");
180#endif
181 unsigned int *strand_number;
182 unsigned int *strand_order;
183 unsigned int *strand_order_uniq;
184 unsigned int *strand_start;
185 unsigned int *strand_end;
187 unsigned int strands;
199 int *iindx;
200 int *jindx;
213 void *auxdata;
228 /* data structure to adjust additional structural domains, such as G-quadruplexes */
231 /* data structure to adjust additional contributions to unpaired stretches, e.g. due to protein binding */
234 /* auxiliary (user-defined) extension to the folding grammar */
241#ifndef VRNA_DISABLE_C11_FEATURES
242 /* C11 support for unnamed unions/structs */
243 union {
244 struct {
245#endif
246
251 char *sequence;
258 short *encoding5;
259 short *encoding3;
260
261 short *sequence_encoding2;
262
263
264 char *ptype;
286#ifndef VRNA_DISABLE_C11_FEATURES
287 /* C11 support for unnamed unions/structs */
288};
289struct {
290#endif
291
296 char **sequences;
300 unsigned int n_seq;
303 char *cons_seq;
306 short *S_cons;
309 short **S;
312 short **S5;
315 short **S3;
318 char **Ss;
319 unsigned int **a2s;
320 int *pscore;
333 int oldAliEn;
334
338#ifndef VRNA_DISABLE_C11_FEATURES
339};
340};
341#endif
342
349 unsigned int maxD1;
350 unsigned int maxD2;
354 unsigned int *referenceBPs1;
355 unsigned int *referenceBPs2;
356 unsigned int *bpdist;
358 unsigned int *mm1;
359 unsigned int *mm2;
372 char **ptype_local;
373#ifdef VRNA_WITH_SVM
374 vrna_zsc_dat_t zscore_data;
375#endif
376
380};
381
382
383/* the definitions below should be used for functions that return/receive/destroy fold compound data structures */
384
388#define VRNA_OPTION_DEFAULT 0U
389
396#define VRNA_OPTION_MFE 1U
397
404#define VRNA_OPTION_PF 2U
405
409#define VRNA_OPTION_HYBRID 4U
410
420#define VRNA_OPTION_EVAL_ONLY 8U
421
425#define VRNA_OPTION_WINDOW 16U
426
465vrna_fold_compound(const char *sequence,
466 const vrna_md_t *md_p,
467 unsigned int options);
468
469
508vrna_fold_compound_comparative(const char **sequences,
509 vrna_md_t *md_p,
510 unsigned int options);
511
512
514vrna_fold_compound_comparative2(const char **sequences,
515 const char **names,
516 const unsigned char *orientation,
517 const unsigned long long *start,
518 const unsigned long long *genome_size,
519 vrna_md_t *md_p,
520 unsigned int options);
521
522
524vrna_fold_compound_TwoD(const char *sequence,
525 const char *s1,
526 const char *s2,
527 vrna_md_t *md_p,
528 unsigned int options);
529
530
531int
532vrna_fold_compound_prepare(vrna_fold_compound_t *fc,
533 unsigned int options);
534
535
543void
545
546
564void
566 void *data,
568
569
585void
588
589
594#endif
Functions to deal with standard dynamic programming (DP) matrices.
Implementations for the RNA folding grammar.
Definition sequence.h:52
Data structure representing a nucleotide sequence.
Definition sequence.h:41
Data structure to store all functionality for ligand binding.
Definition unstructured_domains.h:281
Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_f...
Definition dp_matrices.h:47
Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fol...
Definition dp_matrices.h:207
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition basic.h:110
The datastructure that contains temperature scaled energy parameters.
Definition basic.h:57
vrna_auxdata_free_f free_auxdata
A callback to free auxiliary user data whenever the fold_compound itself is free'd.
Definition fold_compound.h:217
vrna_msa_t * alignment
Set of alignments.
Definition fold_compound.h:189
unsigned int * mm1
Maximum matching matrix, reference struct 1 disallowed.
Definition fold_compound.h:358
int * pscore
Precomputed array of pair types expressed as pairing scores.
Definition fold_compound.h:320
unsigned int * referenceBPs2
Matrix containing number of basepairs of reference structure2 in interval [i,j].
Definition fold_compound.h:355
vrna_param_t * params
The precomputed free energy contributions for each type of loop.
Definition fold_compound.h:196
void * auxdata
A pointer to auxiliary, user-defined data.
Definition fold_compound.h:213
unsigned int * strand_number
The strand number a particular nucleotide is associated with.
Definition fold_compound.h:181
char ** ptype_local
Pair type array (for local folding)
Definition fold_compound.h:372
unsigned int maxD2
Maximum allowed base pair distance to second reference.
Definition fold_compound.h:350
const vrna_fc_type_e type
The type of the vrna_fold_compound_t.
Definition fold_compound.h:166
unsigned int * strand_order
The strand order, i.e. permutation of current concatenated sequence.
Definition fold_compound.h:182
char * ptype
Pair type array.
Definition fold_compound.h:264
unsigned int maxD1
Maximum allowed base pair distance to first reference.
Definition fold_compound.h:349
vrna_gr_aux_t * aux_grammar
Additional decomposition grammar rules.
Definition fold_compound.h:235
vrna_ud_t * domains_up
Additional unstructured domains.
Definition fold_compound.h:232
int * jindx
DP matrix accessor
Definition fold_compound.h:200
unsigned int * mm2
Maximum matching matrix, reference struct 2 disallowed.
Definition fold_compound.h:359
unsigned int * strand_start
The start position of a particular strand within the current concatenated sequence.
Definition fold_compound.h:184
unsigned int * bpdist
Matrix containing base pair distance of reference structure 1 and 2 on interval [i,...
Definition fold_compound.h:356
unsigned int n_seq
The number of sequences in the alignment.
Definition fold_compound.h:300
unsigned int * referenceBPs1
Matrix containing number of basepairs of reference structure1 in interval [i,j].
Definition fold_compound.h:354
vrna_exp_param_t * exp_params
The precomputed free energy contributions as Boltzmann factors
Definition fold_compound.h:197
short ** S5
S5[s][i] holds next base 5' of i in sequence s.
Definition fold_compound.h:312
char * ptype_pf_compat
ptype array indexed via iindx
Definition fold_compound.h:273
vrna_seq_t * nucleotides
Set of nucleotide sequences.
Definition fold_compound.h:188
char * sequence
The input sequence string.
Definition fold_compound.h:251
short * reference_pt2
A pairtable of the second reference structure.
Definition fold_compound.h:352
unsigned int length
The length of the sequence (or sequence alignment)
Definition fold_compound.h:173
char ** sequences
The aligned sequences.
Definition fold_compound.h:296
short * sequence_encoding
Numerical encoding of the input sequence.
Definition fold_compound.h:254
short * reference_pt1
A pairtable of the first reference structure.
Definition fold_compound.h:351
short * S_cons
Numerical encoding of the consensus sequence.
Definition fold_compound.h:306
unsigned int * strand_end
The end (last) position of a particular strand within the current concatenated sequence.
Definition fold_compound.h:185
vrna_zsc_dat_t zscore_data
Data structure with settings for z-score computations.
Definition fold_compound.h:374
short * pscore_pf_compat
Precomputed array of pair types expressed as pairing scores indexed via iindx.
Definition fold_compound.h:326
vrna_sd_t * domains_struc
Additional structured domains.
Definition fold_compound.h:229
vrna_sc_t ** scs
A set of soft constraints (for each sequence in the alignment)
Definition fold_compound.h:330
char * cons_seq
The consensus sequence of the aligned sequences.
Definition fold_compound.h:303
vrna_sc_t * sc
The soft constraints for usage in structure prediction and evaluation.
Definition fold_compound.h:278
vrna_mx_mfe_t * matrices
The MFE DP matrices.
Definition fold_compound.h:193
vrna_hc_t * hc
The hard constraints data structure used for structure prediction.
Definition fold_compound.h:191
unsigned int strands
Number of interacting strands.
Definition fold_compound.h:187
int ** pscore_local
Precomputed array of pair types expressed as pairing scores.
Definition fold_compound.h:323
int window_size
window size for local folding sliding window approach
Definition fold_compound.h:371
int cutpoint
The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint,...
Definition fold_compound.h:176
short ** S
Numerical encoding of the sequences in the alignment.
Definition fold_compound.h:309
vrna_recursion_status_f stat_cb
Recursion status callback (usually called just before, and after recursive computations in the librar...
Definition fold_compound.h:208
unsigned int * strand_order_uniq
The strand order array where identical sequences have the same ID.
Definition fold_compound.h:183
short ** S3
Sl[s][i] holds next base 3' of i in sequence s.
Definition fold_compound.h:315
vrna_mx_pf_t * exp_matrices
The PF DP matrices
Definition fold_compound.h:194
int * iindx
DP matrix accessor
Definition fold_compound.h:199
vrna_fc_type_e
An enumerator that is used to specify the type of a vrna_fold_compound_t.
Definition fold_compound.h:143
void vrna_fold_compound_free(vrna_fold_compound_t *fc)
Free memory occupied by a vrna_fold_compound_t.
void vrna_fold_compound_add_callback(vrna_fold_compound_t *fc, vrna_recursion_status_f f)
Add a recursion status callback to the vrna_fold_compound_t.
void() vrna_callback_free_auxdata(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition fold_compound.h:66
void(* vrna_auxdata_free_f)(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition fold_compound.h:58
vrna_fold_compound_t * vrna_fold_compound(const char *sequence, const vrna_md_t *md_p, unsigned int options)
Retrieve a vrna_fold_compound_t data structure for single sequences and hybridizing sequences.
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.
void vrna_fold_compound_add_auxdata(vrna_fold_compound_t *fc, void *data, vrna_auxdata_free_f f)
Add auxiliary data to the vrna_fold_compound_t.
void(* vrna_recursion_status_f)(unsigned char status, void *data)
Callback to perform specific user-defined actions before, or after recursive computations.
Definition fold_compound.h:86
@ VRNA_FC_TYPE_SINGLE
Definition fold_compound.h:144
@ VRNA_FC_TYPE_COMPARATIVE
Definition fold_compound.h:145
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:161
Definition grammar.h:57
The hard constraints data structure.
Definition hard.h:377
The data structure that contains the complete model details used throughout the calculations.
Definition model.h:245
The soft constraints data structure.
Definition soft.h:211
Functions and data structures for handling of secondary structure hard constraints.
The model details data structure and its corresponding modifiers.
Functions to deal with sets of energy parameters.
Functions and data structures related to sequence representations ,.
Functions and data structures for secondary structure soft constraints.
This module provides interfaces that deal with additional structured domains in the folding grammar.
Definition structured_domains.h:26
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.