RNAlib-2.4.8
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 
24 
36 typedef struct vrna_hc_s vrna_hc_t;
37 
42 typedef struct vrna_hc_up_s vrna_hc_up_t;
43 
75 typedef unsigned char (vrna_callback_hc_evaluate)(int i,
76  int j,
77  int k,
78  int l,
79  unsigned char d,
80  void *data);
81 
87 #define VRNA_CONSTRAINT_NO_HEADER 0
88 
97 #define VRNA_CONSTRAINT_DB 16384U
98 
110 #define VRNA_CONSTRAINT_DB_ENFORCE_BP 32768U
111 
123 #define VRNA_CONSTRAINT_DB_PIPE 65536U
124 
133 #define VRNA_CONSTRAINT_DB_DOT 131072U
134 
142 #define VRNA_CONSTRAINT_DB_X 262144U
143 
149 #define VRNA_CONSTRAINT_DB_ANG_BRACK 524288U
150 
158 #define VRNA_CONSTRAINT_DB_RND_BRACK 1048576U
159 
171 #define VRNA_CONSTRAINT_DB_INTRAMOL 2097152U
172 
184 #define VRNA_CONSTRAINT_DB_INTERMOL 4194304U
185 
196 #define VRNA_CONSTRAINT_DB_GQUAD 8388608U
197 
198 #define VRNA_CONSTRAINT_DB_CANONICAL_BP 16777216U
199 
208 #define VRNA_CONSTRAINT_DB_WUSS 33554432U
209 
210 
222 #define VRNA_CONSTRAINT_DB_DEFAULT \
223  (VRNA_CONSTRAINT_DB \
224  | VRNA_CONSTRAINT_DB_PIPE \
225  | VRNA_CONSTRAINT_DB_DOT \
226  | VRNA_CONSTRAINT_DB_X \
227  | VRNA_CONSTRAINT_DB_ANG_BRACK \
228  | VRNA_CONSTRAINT_DB_RND_BRACK \
229  | VRNA_CONSTRAINT_DB_INTRAMOL \
230  | VRNA_CONSTRAINT_DB_INTERMOL \
231  | VRNA_CONSTRAINT_DB_GQUAD \
232  )
233 
240 #define VRNA_CONSTRAINT_CONTEXT_EXT_LOOP (unsigned char)0x01
241 
248 #define VRNA_CONSTRAINT_CONTEXT_HP_LOOP (unsigned char)0x02
249 
256 #define VRNA_CONSTRAINT_CONTEXT_INT_LOOP (unsigned char)0x04
257 
264 #define VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC (unsigned char)0x08
265 
272 #define VRNA_CONSTRAINT_CONTEXT_MB_LOOP (unsigned char)0x10
273 
280 #define VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC (unsigned char)0x20
281 
285 #define VRNA_CONSTRAINT_CONTEXT_ENFORCE (unsigned char)0x40
286 
290 #define VRNA_CONSTRAINT_CONTEXT_NO_REMOVE (unsigned char)0x80
291 
292 
296 #define VRNA_CONSTRAINT_CONTEXT_NONE (unsigned char)0
297 
301 #define VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_EXT_LOOP | \
302  VRNA_CONSTRAINT_CONTEXT_HP_LOOP | \
303  VRNA_CONSTRAINT_CONTEXT_INT_LOOP | \
304  VRNA_CONSTRAINT_CONTEXT_MB_LOOP)
305 
309 #define VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC | \
310  VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)
311 
318 #define VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS | \
319  VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS)
320 
321 
328 typedef enum {
335 
336 
340 typedef struct {
341  int interval_start;
342  int interval_end;
343  unsigned char loop_type;
344  unsigned char replace : 1;
346 
371 struct vrna_hc_s {
372  vrna_hc_type_e type;
373  unsigned int n;
374 
375 #ifndef VRNA_DISABLE_C11_FEATURES
376  /* C11 support for unnamed unions/structs */
377  union {
378  struct {
379 #endif
380  unsigned char *matrix;
383 #ifndef VRNA_DISABLE_C11_FEATURES
384  };
385  struct {
386 #endif
387  unsigned char **matrix_local;
388  unsigned char *up_storage;
389  vrna_hc_bp_storage_t **bp_storage;
390 #ifndef VRNA_DISABLE_C11_FEATURES
391  };
392  };
393 #endif
394 
395  int *up_ext;
398  int *up_hp;
401  int *up_int;
404  int *up_ml;
412  void *data;
427 };
428 
434 struct vrna_hc_up_s {
435  int position;
436  unsigned char options;
437 };
438 
461 void vrna_message_constraint_options(unsigned int option);
462 
463 
475 
476 
492 
493 
494 void vrna_hc_init_window(vrna_fold_compound_t *vc);
495 
496 
497 void
498 vrna_hc_update(vrna_fold_compound_t *fc,
499  unsigned int i);
500 
501 
517  int i,
518  unsigned char option);
519 
520 
530 int
532  vrna_hc_up_t *constraints);
533 
534 
552  int i,
553  int j,
554  unsigned char option);
555 
556 
575  int i,
576  int d,
577  unsigned char option);
578 
579 
591 void vrna_hc_free(vrna_hc_t *hc);
592 
593 
600 
601 
614  void *data,
616 
617 
636 int
638  const char *constraint,
639  unsigned int options);
640 
641 
642 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
643 
651 DEPRECATED(void print_tty_constraint(unsigned int option),
652  "Use vrna_message_constraint_options() instead");
653 
660 DEPRECATED(void print_tty_constraint_full(void),
661  "Use vrna_message_constraint_options_all() instead");
662 
675 DEPRECATED(void constrain_ptypes(const char *constraint,
676  unsigned int length,
677  char *ptype,
678  int *BP,
679  int min_loop_size,
680  unsigned int idx_type),
681  "Use the new API and the hard constraint framework instead");
682 
683 #endif
684 
685 #endif
unsigned char options
The hard constraint option.
Definition: hard.h:436
void print_tty_constraint(unsigned int option)
Print structure constraint characters to stdout. (constraint support is specified by option parameter...
int * up_hp
A linear array that holds the number of allowed unpaired nucleotides in a hairpin loop...
Definition: hard.h:398
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.
Hard Constraints suitable for local structure prediction using window approach.
Definition: hard.h:330
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.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
Default Hard Constraints.
Definition: hard.h:329
int * up_ml
A linear array that holds the number of allowed unpaired nucleotides in a multi branched loop...
Definition: hard.h:404
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:75
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)
void vrna_message_constraint_options_all(void)
Print structure constraint characters to stdout (full constraint support)
Various data structures and pre-processor macros.
Functions and data structures for constraining secondary structure predictions and evaluation...
A single hard constraint for a single nucleotide.
Definition: hard.h:434
vrna_callback_hc_evaluate * f
A function pointer that returns whether or not a certain decomposition may be evaluated.
Definition: hard.h:408
void * data
A pointer to some structure where the user may store necessary data to evaluate its generic hard cons...
Definition: hard.h:412
unsigned char * matrix
Upper triangular matrix that encodes where a base pair or unpaired nucleotide is allowed.
Definition: hard.h:380
The hard constraints data structure.
Definition: hard.h:371
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.
int * up_ext
A linear array that holds the number of allowed unpaired nucleotides in an exterior loop...
Definition: hard.h:395
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.
void() vrna_callback_free_auxdata(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: fold_compound.h:46
int * up_int
A linear array that holds the number of allowed unpaired nucleotides in an interior loop...
Definition: hard.h:401
vrna_hc_type_e
The hard constraints type.
Definition: hard.h:328
void print_tty_constraint_full(void)
Print structure constraint characters to stdout (full constraint support)
A base pair hard constraint.
Definition: hard.h:340
void vrna_message_constraint_options(unsigned int option)
Print a help message for pseudo dot-bracket structure constraint characters to stdout. (constraint support is specified by option parameter)
void vrna_hc_add_bp(vrna_fold_compound_t *vc, int i, int j, unsigned char option)
Favorize/Enforce a certain base pair (i,j)
vrna_callback_free_auxdata * free_data
A pointer to a function to free memory occupied by auxiliary data.
Definition: hard.h:417
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.
int position
The sequence position (1-based)
Definition: hard.h:435
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.
void vrna_hc_free(vrna_hc_t *hc)
Free the memory allocated by a vrna_hc_t data structure.