RNAlib-2.2.0RC0
aln_util.h
1 #ifndef __VIENNA_RNA_PACKAGE_ALN_UTIL_H__
2 #define __VIENNA_RNA_PACKAGE_ALN_UTIL_H__
3 
4 #ifdef __GNUC__
5 #define DEPRECATED(func) func __attribute__ ((deprecated))
6 #else
7 #define DEPRECATED(func) func
8 #endif
9 
10 int read_clustal( FILE *clust,
11  char *AlignedSeqs[],
12  char *names[]);
13 /*@only@*/ /*@notnull@*/ char *consensus(const char *AS[]);
14 /*@only@*/ /*@notnull@*/ char *consens_mis(const char *AS[]);
15 
16 char *
17 get_ungapped_sequence(const char *seq);
18 
30 int vrna_ali_get_mpi( char *Alseq[],
31  int n_seq,
32  int length,
33  int *mini);
34 
48 DEPRECATED(int get_mpi(char *Alseq[], int n_seq, int length, int *mini));
49 
50 /*
51 #############################################################
52 # some helper functions that might be useful in the library #
53 #############################################################
54 */
55 
72 void encode_ali_sequence( const char *sequence,
73  short *S,
74  short *s5,
75  short *s3,
76  char *ss,
77  unsigned short *as,
78  int circ);
79 
97 void alloc_sequence_arrays(const char **sequences,
98  short ***S,
99  short ***S5,
100  short ***S3,
101  unsigned short ***a2s,
102  char ***Ss,
103  int circ);
104 
121 void free_sequence_arrays( unsigned int n_seq,
122  short ***S,
123  short ***S5,
124  short ***S3,
125  unsigned short ***a2s,
126  char ***Ss);
127 
128 
129 
130 #endif
int vrna_ali_get_mpi(char *Alseq[], int n_seq, int length, int *mini)
Get the mean pairwise identity in steps from ?to?(ident)
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.
int circ
backward compatibility variable.. this does not effect anything
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.