1 #ifndef VIENNA_RNA_PACKAGE_ALN_UTIL_H
2 #define VIENNA_RNA_PACKAGE_ALN_UTIL_H
5 #define DEPRECATED(func) func __attribute__ ((deprecated))
7 #define DEPRECATED(func) func
10 int read_clustal( FILE *clust,
13 char *consensus(
const char *AS[]);
14 char *consens_mis(
const char *AS[]);
17 get_ungapped_sequence(
const char *seq);
48 DEPRECATED(
int get_mpi(
char *Alseq[],
int n_seq,
int length,
int *mini));
101 unsigned short ***a2s,
125 unsigned short ***a2s,
int vrna_ali_get_mpi(char *Alseq[], int n_seq, int length, int *mini)
Get the mean pairwise identity in steps from ?to?(ident)
int circ
backward compatibility variable.. this does not effect anything
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.
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.