1#ifndef VIENNA_RNA_PACKAGE_RNASTRUCT_H
2#define VIENNA_RNA_PACKAGE_RNASTRUCT_H
4#ifdef VRNA_WARN_DEPRECATED
6# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
7# elif defined(__GNUC__)
8# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
10# define DEPRECATED(func, msg) func
13# define DEPRECATED(func, msg) func
52DEPRECATED(
char *
b2HIT(
const char *structure),
53 "Use vrna_db_to_tree_string() instead!");
66DEPRECATED(
char *
b2C(
const char *structure),
67 "Use vrna_db_to_tree_string() instead!");
81DEPRECATED(
char *
b2Shapiro(
const char *structure),
82 "Use vrna_db_to_tree_string() instead!");
91DEPRECATED(
char *
add_root(
const char *structure),
103 "Use vrna_db_to_tree_string() instead!");
114DEPRECATED(
char *
expand_Full(
const char *structure),
115 "Use vrna_db_to_tree_string() instead!");
126 "Use vrna_tree_string_to_db() instead!");
135DEPRECATED(
char *
unweight(
const char *wcoarse),
136 "Use vrna_tree_string_unweight() instead!");
187DEPRECATED(
extern int loops,
199DEPRECATED(
extern int pairs,
char * expand_Shapiro(const char *coarse)
Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C().
int loop_degree[2000]
contains the corresponding list of loop degrees.
void unexpand_aligned_F(char *align[2])
Converts two aligned structures in expanded notation.
char * b2Shapiro(const char *structure)
Converts the full structure from bracket notation to the weighted coarse grained notation using the '...
int loop_size[2000]
contains a list of all loop sizes. loop_size[0] contains the number of external bases.
void parse_structure(const char *structure)
Collects a statistic of structure elements of the full structure in bracket notation.
int helix_size[2000]
contains a list of all stack sizes.
int loops
contains the number of loops ( and therefore of stacks ).
char * unweight(const char *wcoarse)
Strip weights from any weighted tree.
int pairs
contains the number of base pairs in the last parsed structure.
char * expand_Full(const char *structure)
Convert the full structure from bracket notation to the expanded notation including root.
char * b2C(const char *structure)
Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' ...
char * b2HIT(const char *structure)
Converts the full structure from bracket notation to the HIT notation including root.
char * unexpand_Full(const char *ffull)
Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifi...
int unpaired
contains the number of unpaired bases.
char * add_root(const char *structure)
Adds a root to an un-rooted tree in any except bracket notation.