RNAlib-2.4.14
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 
52 DEPRECATED(char *b2HIT(const char *structure),
53  "Use vrna_db_to_tree_string() instead!"); /* Full -> HIT [incl. root] */
54 
55 
66 DEPRECATED(char *b2C(const char *structure),
67  "Use vrna_db_to_tree_string() instead!"); /* Full -> Coarse [incl. root] */
68 
69 
81 DEPRECATED(char *b2Shapiro(const char *structure),
82  "Use vrna_db_to_tree_string() instead!"); /* Full -> weighted Shapiro [i.r.] */
83 
84 
91 DEPRECATED(char *add_root(const char *structure),
92  ""); /* {Tree} -> ({Tree}R) */
93 
94 
102 DEPRECATED(char *expand_Shapiro(const char *coarse),
103  "Use vrna_db_to_tree_string() instead!");
104 
105 
106 /* add S for stacks to coarse struct */
114 DEPRECATED(char *expand_Full(const char *structure),
115  "Use vrna_db_to_tree_string() instead!"); /* Full -> FFull */
116 
117 
125 DEPRECATED(char *unexpand_Full(const char *ffull),
126  "Use vrna_tree_string_to_db() instead!"); /* FFull -> Full */
127 
128 
135 DEPRECATED(char *unweight(const char *wcoarse),
136  "Use vrna_tree_string_unweight() instead!"); /* remove weights from coarse struct */
137 
138 
148 DEPRECATED(void unexpand_aligned_F(char *align[2]),
149  "");
150 
151 
162 DEPRECATED(void parse_structure(const char *structure),
163  ""); /* make structure statistics */
164 
165 
170 DEPRECATED(extern int loop_size[STRUC],
171  ""); /* loop sizes of a structure */
172 
176 DEPRECATED(extern int helix_size[STRUC],
177  ""); /* helix sizes of a structure */
178 
182 DEPRECATED(extern int loop_degree[STRUC],
183  ""); /* loop degrees of a structure */
184 
188 DEPRECATED(extern int loops,
189  ""); /* n of loops and stacks */
190 
194 DEPRECATED(extern int unpaired,
195  "");
196 
200 DEPRECATED(extern int pairs,
201  ""); /* n of unpaired digits and pairs */
202 
207 #endif
unexpand_aligned_F
void unexpand_aligned_F(char *align[2])
Converts two aligned structures in expanded notation.
loops
int loops
contains the number of loops ( and therefore of stacks ).
loop_degree
int loop_degree[2000]
contains the corresponding list of loop degrees.
helix_size
int helix_size[2000]
contains a list of all stack sizes.
parse_structure
void parse_structure(const char *structure)
Collects a statistic of structure elements of the full structure in bracket notation.
b2HIT
char * b2HIT(const char *structure)
Converts the full structure from bracket notation to the HIT notation including root.
pairs
int pairs
contains the number of base pairs in the last parsed structure.
b2C
char * b2C(const char *structure)
Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' ...
loop_size
int loop_size[2000]
contains a list of all loop sizes. loop_size[0] contains the number of external bases.
unweight
char * unweight(const char *wcoarse)
Strip weights from any weighted tree.
expand_Shapiro
char * expand_Shapiro(const char *coarse)
Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C()...
unexpand_Full
char * unexpand_Full(const char *ffull)
Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifi...
expand_Full
char * expand_Full(const char *structure)
Convert the full structure from bracket notation to the expanded notation including root...
b2Shapiro
char * b2Shapiro(const char *structure)
Converts the full structure from bracket notation to the weighted coarse grained notation using the '...
add_root
char * add_root(const char *structure)
Adds a root to an un-rooted tree in any except bracket notation.
unpaired
int unpaired
contains the number of unpaired bases.