aln_util.h
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#ifndef VIENNA_RNA_PACKAGE_ALN_UTIL_H
#define VIENNA_RNA_PACKAGE_ALN_UTIL_H
#ifdef DEPRECATION_WARNINGS
# ifdef __GNUC__
# define DEPRECATED(func) func __attribute__ ((deprecated))
# else
# define DEPRECATED(func) func
# endif
#else
# define DEPRECATED(func) func
#endif
typedef struct vrna_pinfo_s vrna_pinfo_t;
/* make this interface backward compatible with RNAlib < 2.2.0 */
#define VRNA_BACKWARD_COMPAT
#ifdef VRNA_BACKWARD_COMPAT
/* the following typedefs are for backward compatibility only */
typedef struct vrna_pinfo_s pair_info;
#endif
struct vrna_pinfo_s {
unsigned i;
unsigned j;
float p;
float ent;
short bp[8];
char comp;
};
int read_clustal( FILE *clust,
char *AlignedSeqs[],
char *names[]);
/*@only@*/ /*@notnull@*/ char *consensus(const char *AS[]);
/*@only@*/ /*@notnull@*/ char *consens_mis(const char *AS[]);
char *
get_ungapped_sequence(const char *seq);
int vrna_aln_mpi( char *Alseq[],
int n_seq,
int length,
int *mini);
vrna_pinfo_t *vrna_aln_pinfo(vrna_fold_compound_t *vc,
const char *structure,
double threshold);
DEPRECATED(int get_mpi(char *Alseq[], int n_seq, int length, int *mini));
/*
#############################################################
# some helper functions that might be useful in the library #
#############################################################
*/
void encode_ali_sequence( const char *sequence,
short *S,
short *s5,
short *s3,
char *ss,
unsigned short *as,
int circ);
void alloc_sequence_arrays(const char **sequences,
short ***S,
short ***S5,
short ***S3,
unsigned short ***a2s,
char ***Ss,
int circ);
void free_sequence_arrays( unsigned int n_seq,
short ***S,
short ***S5,
short ***S3,
unsigned short ***a2s,
char ***Ss);
#endif
vrna_pinfo_s::j
unsigned j
nucleotide position j
Definition: aln_util.h:54
vrna_pinfo_s
A base pair info structure.
Definition: aln_util.h:52
alloc_sequence_arrays
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.
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
vrna_aln_mpi
int vrna_aln_mpi(char *Alseq[], int n_seq, int length, int *mini)
Get the mean pairwise identity in steps from ?to?(ident)
vrna_aln_pinfo
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. ...
vrna_pinfo_s::i
unsigned i
nucleotide position i
Definition: aln_util.h:53
vrna_pinfo_s::comp
char comp
1 iff pair is in mfe structure
Definition: aln_util.h:58
vrna_pinfo_s::p
float p
Probability.
Definition: aln_util.h:55
encode_ali_sequence
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.
get_mpi
int get_mpi(char *Alseq[], int n_seq, int length, int *mini)
Get the mean pairwise identity in steps from ?to?(ident)
vrna_pinfo_s::ent
float ent
Pseudo entropy for .
Definition: aln_util.h:56
free_sequence_arrays
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.
circ
int circ
backward compatibility variable.. this does not effect anything
vrna_pinfo_s::bp
short bp[8]
Frequencies of pair_types.
Definition: aln_util.h:57