1 #ifndef VIENNA_RNA_PACKAGE_ALN_UTIL_H 2 #define VIENNA_RNA_PACKAGE_ALN_UTIL_H 4 #ifdef DEPRECATION_WARNINGS 6 # define DEPRECATED(func) func __attribute__ ((deprecated)) 8 # define DEPRECATED(func) func 11 # define DEPRECATED(func) func 30 #define VRNA_BACKWARD_COMPAT 33 #ifdef VRNA_BACKWARD_COMPAT 64 int read_clustal( FILE *clust,
68 char *consensus(
const char *AS[]);
70 char *consens_mis(
const char *AS[]);
73 get_ungapped_sequence(
const char *seq);
99 const char *structure,
103 vrna_aln_pscore(
const char **alignment,
120 DEPRECATED(
int get_mpi(
char *Alseq[],
int n_seq,
int length,
int *mini));
173 unsigned short ***a2s,
197 unsigned short ***a2s,
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