RNAlib-2.4.3
constraints_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 # ifdef __GNUC__
6 # define DEPRECATED(func) func __attribute__ ((deprecated))
7 # else
8 # define DEPRECATED(func) func
9 # endif
10 #else
11 # define DEPRECATED(func) func
12 #endif
13 
14 
15 /* make this interface backward compatible with RNAlib < 2.2.0 */
16 #define VRNA_BACKWARD_COMPAT
17 
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 
210 #define VRNA_CONSTRAINT_DB_WUSS 33554432U
211 
212 
224 #define VRNA_CONSTRAINT_DB_DEFAULT \
225  (VRNA_CONSTRAINT_DB \
226  | VRNA_CONSTRAINT_DB_PIPE \
227  | VRNA_CONSTRAINT_DB_DOT \
228  | VRNA_CONSTRAINT_DB_X \
229  | VRNA_CONSTRAINT_DB_ANG_BRACK \
230  | VRNA_CONSTRAINT_DB_RND_BRACK \
231  | VRNA_CONSTRAINT_DB_INTRAMOL \
232  | VRNA_CONSTRAINT_DB_INTERMOL \
233  | VRNA_CONSTRAINT_DB_GQUAD \
234  )
235 
242 #define VRNA_CONSTRAINT_CONTEXT_EXT_LOOP (unsigned char)0x01
243 
250 #define VRNA_CONSTRAINT_CONTEXT_HP_LOOP (unsigned char)0x02
251 
258 #define VRNA_CONSTRAINT_CONTEXT_INT_LOOP (unsigned char)0x04
259 
266 #define VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC (unsigned char)0x08
267 
274 #define VRNA_CONSTRAINT_CONTEXT_MB_LOOP (unsigned char)0x10
275 
282 #define VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC (unsigned char)0x20
283 
287 #define VRNA_CONSTRAINT_CONTEXT_ENFORCE (unsigned char)0x40
288 
292 #define VRNA_CONSTRAINT_CONTEXT_NO_REMOVE (unsigned char)0x80
293 
294 
298 #define VRNA_CONSTRAINT_CONTEXT_NONE (unsigned char)0
299 
303 #define VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_EXT_LOOP | \
304  VRNA_CONSTRAINT_CONTEXT_HP_LOOP | \
305  VRNA_CONSTRAINT_CONTEXT_INT_LOOP | \
306  VRNA_CONSTRAINT_CONTEXT_MB_LOOP)
307 
311 #define VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC | \
312  VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)
313 
320 #define VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS | \
321  VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS)
322 
323 
330 typedef enum {
337 
338 
342 typedef struct {
343  int interval_start;
344  int interval_end;
345  unsigned char loop_type;
346  unsigned char replace : 1;
348 
373 struct vrna_hc_s {
374  vrna_hc_type_e type;
375  unsigned int n;
376 
377 #ifndef VRNA_DISABLE_C11_FEATURES
378  /* C11 support for unnamed unions/structs */
379  union {
380  struct {
381 #endif
382  unsigned char *matrix;
385 #ifndef VRNA_DISABLE_C11_FEATURES
386  };
387  struct {
388 #endif
389  unsigned char **matrix_local;
390  unsigned char *up_storage;
391  vrna_hc_bp_storage_t **bp_storage;
392 #ifndef VRNA_DISABLE_C11_FEATURES
393  };
394  };
395 #endif
396 
397  int *up_ext;
400  int *up_hp;
403  int *up_int;
406  int *up_ml;
414  void *data;
429 };
430 
436 struct vrna_hc_up_s {
437  int position;
438  unsigned char options;
439 };
440 
463 void vrna_message_constraint_options(unsigned int option);
464 
465 
477 
478 
494 
495 
496 void vrna_hc_init_window(vrna_fold_compound_t *vc);
497 
498 
499 void
500 vrna_hc_update(vrna_fold_compound_t *fc,
501  unsigned int i);
502 
503 
519  int i,
520  unsigned char option);
521 
522 
532 int
534  vrna_hc_up_t *constraints);
535 
536 
554  int i,
555  int j,
556  unsigned char option);
557 
558 
577  int i,
578  int d,
579  unsigned char option);
580 
581 
593 void vrna_hc_free(vrna_hc_t *hc);
594 
595 
602 
603 
616  void *data,
618 
619 
638 int
640  const char *constraint,
641  unsigned int options);
642 
643 
644 #ifdef VRNA_BACKWARD_COMPAT
645 
653 DEPRECATED(void print_tty_constraint(unsigned int option));
654 
661 DEPRECATED(void print_tty_constraint_full(void));
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 
682 #endif
683 
684 #endif
unsigned char options
The hard constraint option.
Definition: constraints_hard.h:438
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.
int * up_hp
A linear array that holds the number of allowed unpaired nucleotides in a hairpin loop...
Definition: constraints_hard.h:400
vrna_hc_type_e
The hard constraints type.
Definition: constraints_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:130
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.
int * up_ml
A linear array that holds the number of allowed unpaired nucleotides in a multi branched loop...
Definition: constraints_hard.h:406
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.
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: constraints_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)
Hard Constraints suitable for local structure prediction using window approach.
Definition: constraints_hard.h:332
void vrna_message_constraint_options_all(void)
Print structure constraint characters to stdout (full constraint support)
Various data structures and pre-processor macros.
A single hard constraint for a single nucleotide.
Definition: constraints_hard.h:436
vrna_callback_hc_evaluate * f
A function pointer that returns whether or not a certain decomposition may be evaluated.
Definition: constraints_hard.h:410
void * data
A pointer to some structure where the user may store necessary data to evaluate its generic hard cons...
Definition: constraints_hard.h:414
unsigned char * matrix
Upper triangular matrix that encodes where a base pair or unpaired nucleotide is allowed.
Definition: constraints_hard.h:382
The hard constraints data structure.
Definition: constraints_hard.h:373
int * up_ext
A linear array that holds the number of allowed unpaired nucleotides in an exterior loop...
Definition: constraints_hard.h:397
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: constraints_hard.h:403
A base pair hard constraint.
Definition: constraints_hard.h:342
void print_tty_constraint(unsigned int option)
Print structure constraint characters to stdout. (constraint support is specified by option parameter...
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: constraints_hard.h:419
Default Hard Constraints.
Definition: constraints_hard.h:331
int position
The sequence position (1-based)
Definition: constraints_hard.h:437
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.