RNAlib-2.5.1
RNAstruct.h
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1#ifndef VIENNA_RNA_PACKAGE_RNASTRUCT_H
2#define VIENNA_RNA_PACKAGE_RNASTRUCT_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
40#define STRUC 2000
41
52DEPRECATED(char *b2HIT(const char *structure),
53 "Use vrna_db_to_tree_string() instead!"); /* Full -> HIT [incl. root] */
54
55
66DEPRECATED(char *b2C(const char *structure),
67 "Use vrna_db_to_tree_string() instead!"); /* Full -> Coarse [incl. root] */
68
69
81DEPRECATED(char *b2Shapiro(const char *structure),
82 "Use vrna_db_to_tree_string() instead!"); /* Full -> weighted Shapiro [i.r.] */
83
84
91DEPRECATED(char *add_root(const char *structure),
92 ""); /* {Tree} -> ({Tree}R) */
93
94
102DEPRECATED(char *expand_Shapiro(const char *coarse),
103 "Use vrna_db_to_tree_string() instead!");
104
105
106/* add S for stacks to coarse struct */
114DEPRECATED(char *expand_Full(const char *structure),
115 "Use vrna_db_to_tree_string() instead!"); /* Full -> FFull */
116
117
125DEPRECATED(char *unexpand_Full(const char *ffull),
126 "Use vrna_tree_string_to_db() instead!"); /* FFull -> Full */
127
128
135DEPRECATED(char *unweight(const char *wcoarse),
136 "Use vrna_tree_string_unweight() instead!"); /* remove weights from coarse struct */
137
138
148DEPRECATED(void unexpand_aligned_F(char *align[2]),
149 "");
150
151
161DEPRECATED(void parse_structure(const char *structure),
162 ""); /* make structure statistics */
163
164
169DEPRECATED(extern int loop_size[STRUC],
170 ""); /* loop sizes of a structure */
171
175DEPRECATED(extern int helix_size[STRUC],
176 ""); /* helix sizes of a structure */
177
181DEPRECATED(extern int loop_degree[STRUC],
182 ""); /* loop degrees of a structure */
183
187DEPRECATED(extern int loops,
188 ""); /* n of loops and stacks */
189
193DEPRECATED(extern int unpaired,
194 "");
195
199DEPRECATED(extern int pairs,
200 ""); /* n of unpaired digits and pairs */
201
206#endif
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.