1 #ifndef __VIENNA_RNA_PACKAGE_ALIFOLD_H__
2 #define __VIENNA_RNA_PACKAGE_ALIFOLD_H__
86 float alifold(
const char **strings,
149 const char *structure,
153 float energy_of_ali_gquad_structure(
const char **sequences,
154 const char *structure,
209 unsigned short ***a2s,
233 unsigned short ***a2s,
327 void free_alipf_arrays(
void);
370 unsigned short ***a2s_p,
float alifold(const char **strings, char *structure)
Compute MFE and according consensus structure of an alignment of sequences.
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
float alipf_fold(const char **sequences, char *structure, plist **pl)
The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities and inf...
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
float alipf_fold_par(const char **sequences, char *structure, plist **pl, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: data_structures.h:171
float ** readribosum(char *name)
Read a ribosum or other user-defined scoring matrix.
int get_alipf_arrays(short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p, short **pscore)
Get pointers to (almost) all relavant arrays used in alifold's partition function computation...
void free_alifold_arrays(void)
Free the memory occupied by MFE alifold functions.
float circalifold(const char **strings, char *structure)
Compute MFE and according structure of an alignment of sequences assuming the sequences are circular ...
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
char * alipbacktrack(double *prob)
Sample a consensus secondary structure from the Boltzmann ensemble according its probability ...
double * export_ali_bppm(void)
Get a pointer to the base pair probability array.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:52
float alipf_circ_fold(const char **sequences, char *structure, plist **pl)
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 energy_of_alistruct(const char **sequences, const char *structure, int n_seq, float *energy)
Calculate the free energy of a consensus structure given a set of aligned sequences.
void update_alifold_params(void)
Update the energy parameters for alifold function.