1 #ifndef VIENNA_RNA_PACKAGE_ALN_UTIL_H 2 #define VIENNA_RNA_PACKAGE_ALN_UTIL_H 4 #ifdef VRNA_WARN_DEPRECATED 6 # define DEPRECATED(func) func __attribute__ ((deprecated)) 8 # define DEPRECATED(func) func 11 # define DEPRECATED(func) func 29 #define VRNA_ALN_DEFAULT 0U 30 #define VRNA_ALN_RNA 1U 31 #define VRNA_ALN_DNA 2U 32 #define VRNA_ALN_UPPERCASE 4U 33 #define VRNA_ALN_LOWERCASE 8U 40 #define VRNA_MEASURE_SHANNON_ENTROPY 1U 43 #define VRNA_BACKWARD_COMPAT 46 #ifdef VRNA_BACKWARD_COMPAT 105 const char *structure,
110 vrna_aln_pscore(
const char **alignment,
181 unsigned int options);
200 const char *structure,
224 unsigned int options);
227 #ifdef VRNA_BACKWARD_COMPAT 229 DEPRECATED(
int read_clustal(FILE *clust,
234 DEPRECATED(
char *consensus(
const char *AS[]));
237 DEPRECATED(
char *consens_mis(
const char *AS[]));
240 DEPRECATED(
char *get_ungapped_sequence(
const char *seq));
254 DEPRECATED(
int get_mpi(
char *Alseq[],
307 unsigned short ***a2s,
330 unsigned short ***a2s,
int vrna_aln_mpi(const char **alignment)
Get the mean pairwise identity in steps from ?to?(ident)
char ** vrna_aln_toRNA(const char **alignment)
Create a copy of an alignment where DNA alphabet is replaced by RNA alphabet.
char ** vrna_aln_copy(const char **alignment, unsigned int options)
Make a copy of a multiple sequence alignment.
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 get_mpi(char *Alseq[], int n_seq, int length, int *mini)
Get the mean pairwise identity in steps from ?to?(ident)
unsigned j
nucleotide position j
Definition: aln_util.h:72
A base pair info structure.
Definition: aln_util.h:70
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:130
char ** vrna_aln_uppercase(const char **alignment)
Create a copy of an alignment with only uppercase letters in the sequences.
float * vrna_aln_conservation_col(const char **alignment, const vrna_md_t *md_p, unsigned int options)
Compute nucleotide conservation in an alignment.
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:189
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.
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. ...
float * vrna_aln_conservation_struct(const char **alignment, const char *structure, const vrna_md_t *md)
Compute base pair conservation of a consensus structure.
void vrna_aln_free(char **alignment)
Free memory occupied by a set of aligned sequences.
unsigned i
nucleotide position i
Definition: aln_util.h:71
char comp
1 iff pair is in mfe structure
Definition: aln_util.h:76
float p
Probability.
Definition: aln_util.h:73
char ** vrna_aln_slice(const char **alignment, unsigned int i, unsigned int j)
Slice out a subalignment from a larger alignment.
float ent
Pseudo entropy for .
Definition: aln_util.h:74
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.
The Basic Fold Compound API.
int circ
backward compatibility variable.. this does not effect anything
short bp[8]
Frequencies of pair_types.
Definition: aln_util.h:75