RNAlib-2.5.1
hard.h
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1#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_H
2#define VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_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
16
34typedef struct vrna_hc_s vrna_hc_t;
35
41
42typedef struct vrna_hc_depot_s vrna_hc_depot_t;
43
46
78typedef unsigned char (vrna_callback_hc_evaluate)(int i,
79 int j,
80 int k,
81 int l,
82 unsigned char d,
83 void *data);
84
90#define VRNA_CONSTRAINT_NO_HEADER 0
91
100#define VRNA_CONSTRAINT_DB 16384U
101
113#define VRNA_CONSTRAINT_DB_ENFORCE_BP 32768U
114
126#define VRNA_CONSTRAINT_DB_PIPE 65536U
127
136#define VRNA_CONSTRAINT_DB_DOT 131072U
145#define VRNA_CONSTRAINT_DB_X 262144U
152#define VRNA_CONSTRAINT_DB_ANG_BRACK 524288U
161#define VRNA_CONSTRAINT_DB_RND_BRACK 1048576U
162
174#define VRNA_CONSTRAINT_DB_INTRAMOL 2097152U
175
187#define VRNA_CONSTRAINT_DB_INTERMOL 4194304U
188
199#define VRNA_CONSTRAINT_DB_GQUAD 8388608U
200
201#define VRNA_CONSTRAINT_DB_CANONICAL_BP 16777216U
202
211#define VRNA_CONSTRAINT_DB_WUSS 33554432U
212
213
225#define VRNA_CONSTRAINT_DB_DEFAULT \
226 (VRNA_CONSTRAINT_DB \
227 | VRNA_CONSTRAINT_DB_PIPE \
228 | VRNA_CONSTRAINT_DB_DOT \
229 | VRNA_CONSTRAINT_DB_X \
230 | VRNA_CONSTRAINT_DB_ANG_BRACK \
231 | VRNA_CONSTRAINT_DB_RND_BRACK \
232 | VRNA_CONSTRAINT_DB_INTRAMOL \
233 | VRNA_CONSTRAINT_DB_INTERMOL \
234 | VRNA_CONSTRAINT_DB_GQUAD \
235 )
236
243#define VRNA_CONSTRAINT_CONTEXT_EXT_LOOP (unsigned char)0x01
244
251#define VRNA_CONSTRAINT_CONTEXT_HP_LOOP (unsigned char)0x02
252
259#define VRNA_CONSTRAINT_CONTEXT_INT_LOOP (unsigned char)0x04
260
267#define VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC (unsigned char)0x08
268
275#define VRNA_CONSTRAINT_CONTEXT_MB_LOOP (unsigned char)0x10
276
283#define VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC (unsigned char)0x20
284
288#define VRNA_CONSTRAINT_CONTEXT_ENFORCE (unsigned char)0x40
289
293#define VRNA_CONSTRAINT_CONTEXT_NO_REMOVE (unsigned char)0x80
294
295
299#define VRNA_CONSTRAINT_CONTEXT_NONE (unsigned char)0
300
304#define VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_EXT_LOOP | \
305 VRNA_CONSTRAINT_CONTEXT_HP_LOOP | \
306 VRNA_CONSTRAINT_CONTEXT_INT_LOOP | \
307 VRNA_CONSTRAINT_CONTEXT_MB_LOOP)
308
312#define VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC | \
313 VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)
314
321#define VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS | \
322 VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS)
323
324
325#define VRNA_CONSTRAINT_WINDOW_UPDATE_5 1U
326
327#define VRNA_CONSTRAINT_WINDOW_UPDATE_3 2U
328
335typedef enum {
342
343
368struct vrna_hc_s {
369 vrna_hc_type_e type;
370 unsigned int n;
371
372 unsigned char state;
373
374#ifndef VRNA_DISABLE_C11_FEATURES
375 /* C11 support for unnamed unions/structs */
376 union {
377 struct {
378#endif
379 unsigned char *mx;
380#ifndef VRNA_DISABLE_C11_FEATURES
381 };
382 struct {
383#endif
384 unsigned char **matrix_local;
385#ifndef VRNA_DISABLE_C11_FEATURES
386 };
387 };
388#endif
389
390 int *up_ext;
393 int *up_hp;
396 int *up_int;
399 int *up_ml;
407 void *data;
423 vrna_hc_depot_t *depot;
424};
425
433 int strand;
434 unsigned char options;
435};
436
459void vrna_message_constraint_options(unsigned int option);
460
461
473
474
490
491
492void vrna_hc_init_window(vrna_fold_compound_t *vc);
493
494
495int
496vrna_hc_prepare(vrna_fold_compound_t *fc,
497 unsigned int options);
498
499void
500vrna_hc_update(vrna_fold_compound_t *fc,
501 unsigned int i,
502 unsigned int options);
503
504
520 int i,
521 unsigned char option);
522
523
524int
525vrna_hc_add_up_strand(vrna_fold_compound_t *fc,
526 unsigned int i,
527 unsigned int strand,
528 unsigned char option);
529
539int
541 vrna_hc_up_t *constraints);
542
543int
544vrna_hc_add_up_strand_batch(vrna_fold_compound_t *fc,
545 vrna_hc_up_t *constraints);
546
564 int i,
565 int j,
566 unsigned char option);
567
568
569int
570vrna_hc_add_bp_strand(vrna_fold_compound_t *fc,
571 unsigned int i,
572 unsigned int strand_i,
573 unsigned int j,
574 unsigned int strand_j,
575 unsigned char option);
576
595 int i,
596 int d,
597 unsigned char option);
598
599
612
613
620
621
634 void *data,
636
637
656int
658 const char *constraint,
659 unsigned int options);
660
661
662#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
663
671DEPRECATED(void print_tty_constraint(unsigned int option),
672 "Use vrna_message_constraint_options() instead");
673
680DEPRECATED(void print_tty_constraint_full(void),
681 "Use vrna_message_constraint_options_all() instead");
682
695DEPRECATED(void constrain_ptypes(const char *constraint,
696 unsigned int length,
697 char *ptype,
698 int *BP,
699 int min_loop_size,
700 unsigned int idx_type),
701 "Use the new API and the hard constraint framework instead");
702
703#endif
704
705#endif
Functions and data structures for constraining secondary structure predictions and evaluation.
The Basic Fold Compound API.
void vrna_message_constraint_options(unsigned int option)
Print a help message for pseudo dot-bracket structure constraint characters to stdout....
void vrna_message_constraint_options_all(void)
Print structure constraint characters to stdout (full constraint support)
void() vrna_callback_free_auxdata(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: fold_compound.h:58
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:148
int * up_int
A linear array that holds the number of allowed unpaired nucleotides in an interior loop.
Definition: hard.h:396
unsigned char options
The hard constraint option
Definition: hard.h:434
int * up_ext
A linear array that holds the number of allowed unpaired nucleotides in an exterior loop.
Definition: hard.h:390
int position
The sequence position (1-based)
Definition: hard.h:432
int * up_hp
A linear array that holds the number of allowed unpaired nucleotides in a hairpin loop.
Definition: hard.h:393
vrna_callback_hc_evaluate * f
A function pointer that returns whether or not a certain decomposition may be evaluated.
Definition: hard.h:403
vrna_callback_free_auxdata * free_data
A pointer to a function to free memory occupied by auxiliary data.
Definition: hard.h:412
int * up_ml
A linear array that holds the number of allowed unpaired nucleotides in a multi branched loop.
Definition: hard.h:399
void * data
A pointer to some structure where the user may store necessary data to evaluate its generic hard cons...
Definition: hard.h:407
void vrna_hc_init(vrna_fold_compound_t *vc)
Initialize/Reset hard constraints to default values.
void vrna_hc_add_up(vrna_fold_compound_t *vc, int i, unsigned char option)
Make a certain nucleotide unpaired.
int vrna_hc_add_up_batch(vrna_fold_compound_t *vc, vrna_hc_up_t *constraints)
Apply a list of hard constraints for single nucleotides.
int vrna_hc_add_from_db(vrna_fold_compound_t *vc, const char *constraint, unsigned int options)
Add hard constraints from pseudo dot-bracket notation.
void vrna_hc_free(vrna_hc_t *hc)
Free the memory allocated by a vrna_hc_t data structure.
int vrna_hc_add_bp(vrna_fold_compound_t *vc, int i, int j, unsigned char option)
Favorize/Enforce a certain base pair (i,j)
unsigned char() vrna_callback_hc_evaluate(int i, int j, int k, int l, unsigned char d, void *data)
Callback to evaluate whether or not a particular decomposition step is contributing to the solution s...
Definition: hard.h:78
void vrna_hc_add_bp_nonspecific(vrna_fold_compound_t *vc, int i, int d, unsigned char option)
Enforce a nucleotide to be paired (upstream/downstream)
The hard constraints data structure.
Definition: hard.h:368
A single hard constraint for a single nucleotide.
Definition: hard.h:431
vrna_hc_type_e
The hard constraints type.
Definition: hard.h:335
@ VRNA_HC_DEFAULT
Default Hard Constraints.
Definition: hard.h:336
@ VRNA_HC_WINDOW
Hard Constraints suitable for local structure prediction using window approach.
Definition: hard.h:337
void vrna_hc_add_data(vrna_fold_compound_t *vc, void *data, vrna_callback_free_auxdata *f)
Add an auxiliary data structure for the generic hard constraints callback function.
void constrain_ptypes(const char *constraint, unsigned int length, char *ptype, int *BP, int min_loop_size, unsigned int idx_type)
Insert constraining pair types according to constraint structure string.
void print_tty_constraint(unsigned int option)
Print structure constraint characters to stdout. (constraint support is specified by option parameter...
void print_tty_constraint_full(void)
Print structure constraint characters to stdout (full constraint support)
void vrna_hc_add_f(vrna_fold_compound_t *vc, vrna_callback_hc_evaluate *f)
Add a function pointer pointer for the generic hard constraint feature.