#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_H
#define VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_H
#ifdef VRNA_WARN_DEPRECATED
# if defined(__clang__)
# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
# elif defined(__GNUC__)
# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
# else
# define DEPRECATED(func, msg) func
# endif
#else
# define DEPRECATED(func, msg) func
#endif
/**
* @file constraints/hard.h
* @ingroup hard_constraints
* @brief Functions and data structures for handling of secondary structure hard constraints
*/
#include <ViennaRNA/fold_compound.h>
#include <ViennaRNA/constraints/basic.h>
#ifdef __cplusplus
extern "C" {
#endif
/**
* @addtogroup hard_constraints
*
* @brief This module covers all functionality for hard constraints in secondary
* structure prediction
*/
/**
* @brief Typename for the hard constraints data structure #vrna_hc_s
* @ingroup hard_constraints
*/
typedef struct vrna_hc_s vrna_hc_t;
/**
* @brief Typename for the single nucleotide hard constraint data structure #vrna_hc_up_s
* @ingroup hard_constraints
*/
typedef struct vrna_hc_up_s vrna_hc_up_t;
typedef struct vrna_hc_depot_s vrna_hc_depot_t;
/**
* @brief Callback to evaluate whether or not a particular decomposition step is contributing to the solution space
*
* @ingroup hard_constraints
*
* This is the prototype for callback functions used by the folding recursions to evaluate generic
* hard constraints. The first four parameters passed indicate the delimiting nucleotide positions
* of the decomposition, and the parameter @p denotes the decomposition step. The last parameter
* @p data is the auxiliary data structure associated to the hard constraints via vrna_hc_add_data(),
* or NULL if no auxiliary data was added.
*
* @callback
* @parblock
* This callback enables one to over-rule default hard constraints in secondary structure
* decompositions.
* @endparblock
*
* @see #VRNA_DECOMP_PAIR_HP, #VRNA_DECOMP_PAIR_IL, #VRNA_DECOMP_PAIR_ML, #VRNA_DECOMP_ML_ML_ML,
* #VRNA_DECOMP_ML_STEM, #VRNA_DECOMP_ML_ML, #VRNA_DECOMP_ML_UP, #VRNA_DECOMP_ML_ML_STEM,
* #VRNA_DECOMP_ML_COAXIAL, #VRNA_DECOMP_EXT_EXT, #VRNA_DECOMP_EXT_UP, #VRNA_DECOMP_EXT_STEM,
* #VRNA_DECOMP_EXT_EXT_EXT, #VRNA_DECOMP_EXT_STEM_EXT, #VRNA_DECOMP_EXT_EXT_STEM,
* #VRNA_DECOMP_EXT_EXT_STEM1, vrna_hc_add_f(), vrna_hc_add_data()
*
* @param i Left (5') delimiter position of substructure
* @param j Right (3') delimiter position of substructure
* @param k Left delimiter of decomposition
* @param l Right delimiter of decomposition
* @param d Decomposition step indicator
* @param data Auxiliary data
* @return A non-zero value if the decomposition is valid, 0 otherwise
*/
typedef unsigned char (vrna_callback_hc_evaluate)(int i,
int j,
int k,
int l,
unsigned char d,
void *data);
/**
* @brief do not print the header information line
* @deprecated This mode is not supported anymore!
*
*/
#define VRNA_CONSTRAINT_NO_HEADER 0
/**
* @brief Flag for vrna_constraints_add() to indicate that constraint is passed in pseudo dot-bracket notation
*
* @see vrna_constraints_add(), vrna_message_constraint_options(), vrna_message_constraint_options_all()
*
* @ingroup hard_constraints
*
*/
#define VRNA_CONSTRAINT_DB 16384U
/**
* @brief Switch for dot-bracket structure constraint to enforce base pairs
*
* This flag should be used to really enforce base pairs given in dot-bracket constraint rather than
* just weakly-enforcing them.
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),
* vrna_message_constraint_options_all()
*/
#define VRNA_CONSTRAINT_DB_ENFORCE_BP 32768U
/**
* @brief Flag that is used to indicate the pipe '|' sign in pseudo dot-bracket
* notation of hard constraints.
*
* Use this definition to indicate the pipe sign '|' (paired with another base)
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),
* vrna_message_constraint_options_all()
*/
#define VRNA_CONSTRAINT_DB_PIPE 65536U
/**
* @brief dot '.' switch for structure constraints (no constraint at all)
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),
* vrna_message_constraint_options_all()
*/
#define VRNA_CONSTRAINT_DB_DOT 131072U
/**
* @brief 'x' switch for structure constraint (base must not pair)
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),
* vrna_message_constraint_options_all()
*/
#define VRNA_CONSTRAINT_DB_X 262144U
/**
* @brief angle brackets '<', '>' switch for structure constraint (paired downstream/upstream)
*
* @see vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),
* vrna_message_constraint_options_all()
*/
#define VRNA_CONSTRAINT_DB_ANG_BRACK 524288U
/**
* @brief round brackets '(',')' switch for structure constraint (base i pairs base j)
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),
* vrna_message_constraint_options_all()
*/
#define VRNA_CONSTRAINT_DB_RND_BRACK 1048576U
/**
* @brief Flag that is used to indicate the character 'l' in pseudo dot-bracket
* notation of hard constraints.
*
* Use this definition to indicate the usage of 'l' character (intramolecular pairs only)
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),
* vrna_message_constraint_options_all()
*/
#define VRNA_CONSTRAINT_DB_INTRAMOL 2097152U
/**
* @brief Flag that is used to indicate the character 'e' in pseudo dot-bracket
* notation of hard constraints.
*
* Use this definition to indicate the usage of 'e' character (intermolecular pairs only)
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),
* vrna_message_constraint_options_all()
*/
#define VRNA_CONSTRAINT_DB_INTERMOL 4194304U
/**
* @brief '+' switch for structure constraint (base is involved in a gquad)
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),
* vrna_message_constraint_options_all()
*
* @warning This flag is for future purposes only! No implementation recognizes it yet.
*/
#define VRNA_CONSTRAINT_DB_GQUAD 8388608U
#define VRNA_CONSTRAINT_DB_CANONICAL_BP 16777216U
/**
* @brief Flag to indicate Washington University Secondary Structure (WUSS) notation of the hard constraint string
*
* This secondary structure notation for RNAs is usually used as consensus secondary structure (SS_cons) entry
* in Stockholm formatted files
*
* @ingroup hard_constraints
*/
#define VRNA_CONSTRAINT_DB_WUSS 33554432U
/**
* @brief Switch for dot-bracket structure constraint with default symbols
*
* This flag conveniently combines all possible symbols in dot-bracket notation
* for hard constraints and #VRNA_CONSTRAINT_DB
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),
* vrna_message_constraint_options_all()
*/
#define VRNA_CONSTRAINT_DB_DEFAULT \
(VRNA_CONSTRAINT_DB \
| VRNA_CONSTRAINT_DB_PIPE \
| VRNA_CONSTRAINT_DB_DOT \
| VRNA_CONSTRAINT_DB_X \
| VRNA_CONSTRAINT_DB_ANG_BRACK \
| VRNA_CONSTRAINT_DB_RND_BRACK \
| VRNA_CONSTRAINT_DB_INTRAMOL \
| VRNA_CONSTRAINT_DB_INTERMOL \
| VRNA_CONSTRAINT_DB_GQUAD \
)
/**
* @brief Hard constraints flag, base pair in the exterior loop
*
* @ingroup hard_constraints
*
*/
#define VRNA_CONSTRAINT_CONTEXT_EXT_LOOP (unsigned char)0x01
/**
* @brief Hard constraints flag, base pair encloses hairpin loop
*
* @ingroup hard_constraints
*
*/
#define VRNA_CONSTRAINT_CONTEXT_HP_LOOP (unsigned char)0x02
/**
* @brief Hard constraints flag, base pair encloses an interior loop
*
* @ingroup hard_constraints
*
*/
#define VRNA_CONSTRAINT_CONTEXT_INT_LOOP (unsigned char)0x04
/**
* @brief Hard constraints flag, base pair encloses a multi branch loop
*
* @ingroup hard_constraints
*
*/
#define VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC (unsigned char)0x08
/**
* @brief Hard constraints flag, base pair is enclosed in an interior loop
*
* @ingroup hard_constraints
*
*/
#define VRNA_CONSTRAINT_CONTEXT_MB_LOOP (unsigned char)0x10
/**
* @brief Hard constraints flag, base pair is enclosed in a multi branch loop
*
* @ingroup hard_constraints
*
*/
#define VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC (unsigned char)0x20
/**
* @brief Hard constraint flag to indicate enforcement of constraints
*/
#define VRNA_CONSTRAINT_CONTEXT_ENFORCE (unsigned char)0x40
/**
* @brief Hard constraint flag to indicate not to remove base pairs that conflict with a given constraint
*/
#define VRNA_CONSTRAINT_CONTEXT_NO_REMOVE (unsigned char)0x80
/**
* @brief Constraint context flag that forbids any loop
*/
#define VRNA_CONSTRAINT_CONTEXT_NONE (unsigned char)0
/**
* @brief Constraint context flag indicating base pairs that close any loop
*/
#define VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_EXT_LOOP | \
VRNA_CONSTRAINT_CONTEXT_HP_LOOP | \
VRNA_CONSTRAINT_CONTEXT_INT_LOOP | \
VRNA_CONSTRAINT_CONTEXT_MB_LOOP)
/**
* @brief Constraint context flag indicating base pairs enclosed by any loop
*/
#define VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC | \
VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)
/**
* @brief Constraint context flag indicating any loop context
*
* @ingroup hard_constraints
*
*/
#define VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS | \
VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS)
#define VRNA_CONSTRAINT_WINDOW_UPDATE_5 1U
#define VRNA_CONSTRAINT_WINDOW_UPDATE_3 2U
/**
* @brief The hard constraints type
*
* Global and local structure prediction methods use a slightly different way to
* handle hard constraints internally. This enum is used to distinguish both types.
*/
typedef enum {
VRNA_HC_DEFAULT, /**< @brief Default Hard Constraints */
VRNA_HC_WINDOW /**< @brief Hard Constraints suitable for local structure prediction using
* window approach.
* @see vrna_mfe_window(), vrna_mfe_window_zscore(), pfl_fold()
*/
} vrna_hc_type_e;
/**
* @brief The hard constraints data structure
*
* The content of this data structure determines the decomposition pattern
* used in the folding recursions. Attribute 'matrix' is used as source for
* the branching pattern of the decompositions during all folding recursions.
* Any entry in matrix[i,j] consists of the 6 LSB that allows one to distinguish the
* following types of base pairs:
* - in the exterior loop (#VRNA_CONSTRAINT_CONTEXT_EXT_LOOP)
* - enclosing a hairpin (#VRNA_CONSTRAINT_CONTEXT_HP_LOOP)
* - enclosing an interior loop (#VRNA_CONSTRAINT_CONTEXT_INT_LOOP)
* - enclosed by an exterior loop (#VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC)
* - enclosing a multi branch loop (#VRNA_CONSTRAINT_CONTEXT_MB_LOOP)
* - enclosed by a multi branch loop (#VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)
*
* The four linear arrays 'up_xxx' provide the number of available unpaired
* nucleotides (including position i) 3' of each position in the sequence.
*
* @see vrna_hc_init(), vrna_hc_free(), #VRNA_CONSTRAINT_CONTEXT_EXT_LOOP,
* #VRNA_CONSTRAINT_CONTEXT_HP_LOOP, #VRNA_CONSTRAINT_CONTEXT_INT_LOOP,
* #VRNA_CONSTRAINT_CONTEXT_MB_LOOP, #VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC
*
* @ingroup hard_constraints
*/
struct vrna_hc_s {
vrna_hc_type_e type;
unsigned int n;
unsigned char state;
#ifndef VRNA_DISABLE_C11_FEATURES
/* C11 support for unnamed unions/structs */
union {
struct {
#endif
unsigned char *matrix; /**< @brief Upper triangular matrix that encodes where a
* base pair or unpaired nucleotide is allowed
*/
unsigned char *mx;
#ifndef VRNA_DISABLE_C11_FEATURES
};
struct {
#endif
unsigned char **matrix_local;
#ifndef VRNA_DISABLE_C11_FEATURES
};
};
#endif
int *up_ext; /**< @brief A linear array that holds the number of allowed
* unpaired nucleotides in an exterior loop
*/
int *up_hp; /**< @brief A linear array that holds the number of allowed
* unpaired nucleotides in a hairpin loop
*/
int *up_int; /**< @brief A linear array that holds the number of allowed
* unpaired nucleotides in an interior loop
*/
int *up_ml; /**< @brief A linear array that holds the number of allowed
* unpaired nucleotides in a multi branched loop
*/
vrna_callback_hc_evaluate *f; /**< @brief A function pointer that returns whether or
* not a certain decomposition may be evaluated
*/
void *data; /**< @brief A pointer to some structure where the user
* may store necessary data to evaluate its
* generic hard constraint function
*/
vrna_callback_free_auxdata *free_data; /**< @brief A pointer to a function to free memory
* occupied by auxiliary data
*
* The function this pointer is pointing to will be
* called upon destruction of the #vrna_hc_s, and
* provided with the vrna_hc_s.data pointer that
* may hold auxiliary data. Hence, to avoid leaking
* memory, the user may use this pointer to free
* memory occupied by auxiliary data.
*/
vrna_hc_depot_t *depot;
};
/**
* @brief A single hard constraint for a single nucleotide
*
* @ingroup hard_constraints
*/
struct vrna_hc_up_s {
int position; /**< @brief The sequence position (1-based) */
int strand;
unsigned char options; /**< @brief The hard constraint option */
};
/**
* @brief Print a help message for pseudo dot-bracket structure constraint characters to stdout.
* (constraint support is specified by option parameter)
*
* Currently available options are:\n
* #VRNA_CONSTRAINT_DB_PIPE (paired with another base)\n
* #VRNA_CONSTRAINT_DB_DOT (no constraint at all)\n
* #VRNA_CONSTRAINT_DB_X (base must not pair)\n
* #VRNA_CONSTRAINT_DB_ANG_BRACK (paired downstream/upstream)\n
* #VRNA_CONSTRAINT_DB_RND_BRACK (base i pairs base j)\n
*
* pass a collection of options as one value like this:
* @verbatim vrna_message_constraints(option_1 | option_2 | option_n) @endverbatim
*
* @ingroup constraints
*
* @see vrna_message_constraint_options_all(), vrna_constraints_add(), #VRNA_CONSTRAINT_DB,
* #VRNA_CONSTRAINT_DB_PIPE, #VRNA_CONSTRAINT_DB_DOT, #VRNA_CONSTRAINT_DB_X, #VRNA_CONSTRAINT_DB_ANG_BRACK,
* #VRNA_CONSTRAINT_DB_RND_BRACK, #VRNA_CONSTRAINT_DB_INTERMOL, #VRNA_CONSTRAINT_DB_INTRAMOL
*
* @param option Option switch that tells which constraint help will be printed
*/
void vrna_message_constraint_options(unsigned int option);
/**
* @brief Print structure constraint characters to stdout
* (full constraint support)
*
* @ingroup constraints
*
* @see vrna_message_constraint_options(), vrna_constraints_add(), #VRNA_CONSTRAINT_DB,
* #VRNA_CONSTRAINT_DB_PIPE, #VRNA_CONSTRAINT_DB_DOT, #VRNA_CONSTRAINT_DB_X, #VRNA_CONSTRAINT_DB_ANG_BRACK,
* #VRNA_CONSTRAINT_DB_RND_BRACK, #VRNA_CONSTRAINT_DB_INTERMOL, #VRNA_CONSTRAINT_DB_INTRAMOL
*/
void vrna_message_constraint_options_all(void);
/**
* @brief Initialize/Reset hard constraints to default values
*
* This function resets the hard constraints to their default values, i.e.
* all positions may be unpaired in all contexts, and base pairs are
* allowed in all contexts, if they resemble canonical pairs.
* Previously set hard constraints will be removed before initialization.
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_bp(), vrna_hc_add_bp_nonspecific(), vrna_hc_add_up()
*
* @param vc The fold compound
*/
void vrna_hc_init(vrna_fold_compound_t *vc);
void vrna_hc_init_window(vrna_fold_compound_t *vc);
int
vrna_hc_prepare(vrna_fold_compound_t *fc,
unsigned int options);
void
vrna_hc_update(vrna_fold_compound_t *fc,
unsigned int i,
unsigned int options);
/**
* @brief Make a certain nucleotide unpaired
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_bp(), vrna_hc_add_bp_nonspecific(), vrna_hc_init(),
* #VRNA_CONSTRAINT_CONTEXT_EXT_LOOP, #VRNA_CONSTRAINT_CONTEXT_HP_LOOP,
* #VRNA_CONSTRAINT_CONTEXT_INT_LOOP, #VRNA_CONSTRAINT_CONTEXT_MB_LOOP,
* #VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS
*
* @param vc The #vrna_fold_compound_t the hard constraints are associated with
* @param i The position that needs to stay unpaired (1-based)
* @param option The options flag indicating how/where to store the hard constraints
*/
void vrna_hc_add_up(vrna_fold_compound_t *vc,
int i,
unsigned char option);
int
vrna_hc_add_up_strand(vrna_fold_compound_t *fc,
unsigned int i,
unsigned int strand,
unsigned char option);
/**
* @brief Apply a list of hard constraints for single nucleotides
*
* @ingroup hard_constraints
*
* @param vc The #vrna_fold_compound_t the hard constraints are associated with
* @param constraints The list off constraints to apply, last entry must have position
* attribute set to 0
*/
int
vrna_hc_add_up_batch(vrna_fold_compound_t *vc,
vrna_hc_up_t *constraints);
int
vrna_hc_add_up_strand_batch(vrna_fold_compound_t *fc,
vrna_hc_up_t *constraints);
/**
* @brief Favorize/Enforce a certain base pair (i,j)
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_bp_nonspecific(), vrna_hc_add_up(), vrna_hc_init(),
* #VRNA_CONSTRAINT_CONTEXT_EXT_LOOP, #VRNA_CONSTRAINT_CONTEXT_HP_LOOP,
* #VRNA_CONSTRAINT_CONTEXT_INT_LOOP, #VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC,
* #VRNA_CONSTRAINT_CONTEXT_MB_LOOP, #VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC,
* #VRNA_CONSTRAINT_CONTEXT_ENFORCE, #VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS
*
* @param vc The #vrna_fold_compound_t the hard constraints are associated with
* @param i The 5' located nucleotide position of the base pair (1-based)
* @param j The 3' located nucleotide position of the base pair (1-based)
* @param option The options flag indicating how/where to store the hard constraints
*/
int vrna_hc_add_bp(vrna_fold_compound_t *vc,
int i,
int j,
unsigned char option);
int
vrna_hc_add_bp_strand(vrna_fold_compound_t *fc,
unsigned int i,
unsigned int strand_i,
unsigned int j,
unsigned int strand_j,
unsigned char option);
/**
* @brief Enforce a nucleotide to be paired (upstream/downstream)
*
* @ingroup hard_constraints
*
* @see vrna_hc_add_bp(), vrna_hc_add_up(), vrna_hc_init(),
* #VRNA_CONSTRAINT_CONTEXT_EXT_LOOP, #VRNA_CONSTRAINT_CONTEXT_HP_LOOP,
* #VRNA_CONSTRAINT_CONTEXT_INT_LOOP, #VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC,
* #VRNA_CONSTRAINT_CONTEXT_MB_LOOP, #VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC,
* #VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS
*
* @param vc The #vrna_fold_compound_t the hard constraints are associated with
* @param i The position that needs to stay unpaired (1-based)
* @param d The direction of base pairing (@f$ d < 0 @f$: pairs upstream,
* @f$ d > 0 @f$: pairs downstream, @f$ d == 0 @f$: no direction)
* @param option The options flag indicating in which loop type context the pairs may appear
*/
void vrna_hc_add_bp_nonspecific(vrna_fold_compound_t *vc,
int i,
int d,
unsigned char option);
/**
* @brief Free the memory allocated by a #vrna_hc_t data structure
*
* Use this function to free all memory that was allocated for a data structure
* of type #vrna_hc_t .
*
* @see get_hard_constraints(), #vrna_hc_t
*
* @ingroup hard_constraints
*
*/
void vrna_hc_free(vrna_hc_t *hc);
/**
* @brief Add a function pointer pointer for the generic hard constraint
* feature
*/
void vrna_hc_add_f(vrna_fold_compound_t *vc,
vrna_callback_hc_evaluate *f);
/**
* @brief Add an auxiliary data structure for the generic hard constraints callback function
*
* @ingroup generic_hc
*
* @see vrna_hc_add_f()
*
* @param vc The fold compound the generic hard constraint function should be bound to
* @param data A pointer to the data structure that holds required data for function 'f'
* @param f A pointer to a function that free's the memory occupied by @p data (Maybe @p NULL)
*/
void vrna_hc_add_data(vrna_fold_compound_t *vc,
void *data,
vrna_callback_free_auxdata *f);
/**
* @brief Add hard constraints from pseudo dot-bracket notation
*
* This function allows one to apply hard constraints from a pseudo dot-bracket
* notation. The @p options parameter controls, which characters are recognized
* by the parser. Use the #VRNA_CONSTRAINT_DB_DEFAULT convenience macro, if you
* want to allow all known characters
*
* @ingroup hard_constraints
*
* @see #VRNA_CONSTRAINT_DB_PIPE, #VRNA_CONSTRAINT_DB_DOT, #VRNA_CONSTRAINT_DB_X,
* #VRNA_CONSTRAINT_DB_ANG_BRACK, #VRNA_CONSTRAINT_DB_RND_BRACK, #VRNA_CONSTRAINT_DB_INTRAMOL,
* #VRNA_CONSTRAINT_DB_INTERMOL, #VRNA_CONSTRAINT_DB_GQUAD
*
* @param vc The fold compound
* @param constraint A pseudo dot-bracket notation of the hard constraint.
* @param options The option flags
*/
int
vrna_hc_add_from_db(vrna_fold_compound_t *vc,
const char *constraint,
unsigned int options);
#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
/**
* @brief Print structure constraint characters to stdout.
* (constraint support is specified by option parameter)
*
* @deprecated Use vrna_message_constraints() instead!
* @param option Option switch that tells which constraint help will be printed
*/
DEPRECATED(void print_tty_constraint(unsigned int option),
"Use vrna_message_constraint_options() instead");
/**
* @brief Print structure constraint characters to stdout
* (full constraint support)
*
* @deprecated Use vrna_message_constraint_options_all() instead!
*/
DEPRECATED(void print_tty_constraint_full(void),
"Use vrna_message_constraint_options_all() instead");
/**
* @brief Insert constraining pair types according to constraint structure string
*
* @deprecated Do not use this function anymore! Structure constraints are now handled through #vrna_hc_t and related functions.
*
* @param constraint The structure constraint string
* @param length The actual length of the sequence (constraint may be shorter)
* @param ptype A pointer to the basepair type array
* @param BP (not used anymore)
* @param min_loop_size The minimal loop size (usually #TURN )
* @param idx_type Define the access type for base pair type array (0 = indx, 1 = iindx)
*/
DEPRECATED(void constrain_ptypes(const char *constraint,
unsigned int length,
char *ptype,
int *BP,
int min_loop_size,
unsigned int idx_type),
"Use the new API and the hard constraint framework instead");
#endif
#ifdef __cplusplus
}
#endif
#endif
