RNAlib-2.3.1
aln_util.h
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1 #ifndef VIENNA_RNA_PACKAGE_ALN_UTIL_H
2 #define VIENNA_RNA_PACKAGE_ALN_UTIL_H
3 
4 #ifdef DEPRECATION_WARNINGS
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 
27 typedef struct vrna_pinfo_s vrna_pinfo_t;
28 
29 /* make this interface backward compatible with RNAlib < 2.2.0 */
30 #define VRNA_BACKWARD_COMPAT
31 
32 
33 #ifdef VRNA_BACKWARD_COMPAT
34 
35 /* the following typedefs are for backward compatibility only */
36 
41 typedef struct vrna_pinfo_s pair_info;
42 
43 #endif
44 
55 struct vrna_pinfo_s {
56  unsigned i;
57  unsigned j;
58  float p;
59  float ent;
60  short bp[8];
61  char comp;
62 };
63 
64 int read_clustal( FILE *clust,
65  char *AlignedSeqs[],
66  char *names[]);
67 
68 char *consensus(const char *AS[]);
69 
70 char *consens_mis(const char *AS[]);
71 
72 char *
73 get_ungapped_sequence(const char *seq);
74 
83 int vrna_aln_mpi( const char **alignment);
84 
99  const char *structure,
100  double threshold);
101 
102 int *
103 vrna_aln_pscore(const char **alignment,
104  vrna_md_t *md);
105 
106 
120 DEPRECATED(int get_mpi(char *Alseq[], int n_seq, int length, int *mini));
121 
122 /*
123 #############################################################
124 # some helper functions that might be useful in the library #
125 #############################################################
126 */
127 
144 void encode_ali_sequence( const char *sequence,
145  short *S,
146  short *s5,
147  short *s3,
148  char *ss,
149  unsigned short *as,
150  int circ);
151 
169 void alloc_sequence_arrays(const char **sequences,
170  short ***S,
171  short ***S5,
172  short ***S3,
173  unsigned short ***a2s,
174  char ***Ss,
175  int circ);
176 
193 void free_sequence_arrays( unsigned int n_seq,
194  short ***S,
195  short ***S5,
196  short ***S3,
197  unsigned short ***a2s,
198  char ***Ss);
199 
200 
206 #endif
unsigned j
nucleotide position j
Definition: aln_util.h:57
short bp[8]
Frequencies of pair_types.
Definition: aln_util.h:60
unsigned i
nucleotide position i
Definition: aln_util.h:56
void alloc_sequence_arrays(const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ)
Allocate memory for sequence array used to deal with aligned sequences.
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:454
float ent
Pseudo entropy for .
Definition: aln_util.h:59
vrna_pinfo_t * vrna_aln_pinfo(vrna_fold_compound_t *vc, const char *structure, double threshold)
Retrieve an array of vrna_pinfo_t structures from precomputed pair probabilities. ...
A base pair info structure.
Definition: aln_util.h:55
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:191
int vrna_aln_mpi(const char **alignment)
Get the mean pairwise identity in steps from ?to?(ident)
void encode_ali_sequence(const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ)
Get arrays with encoded sequence of the alignment.
int get_mpi(char *Alseq[], int n_seq, int length, int *mini)
Get the mean pairwise identity in steps from ?to?(ident)
void free_sequence_arrays(unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)
Free the memory of the sequence arrays used to deal with aligned sequences.
float p
Probability.
Definition: aln_util.h:58
int circ
backward compatibility variable.. this does not effect anything
char comp
1 iff pair is in mfe structure
Definition: aln_util.h:61