1#ifndef __VIENNA_RNA_PACKAGE_ALIFOLD_H__
2#define __VIENNA_RNA_PACKAGE_ALIFOLD_H__
149 const char *structure,
153float energy_of_ali_gquad_structure(
const char **sequences,
154 const char *structure,
209 unsigned short ***a2s,
233 unsigned short ***a2s,
327void free_alipf_arrays(
void);
370 unsigned short ***a2s_p,
void update_alifold_params(void)
Update the energy parameters for alifold function.
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
int circ
backward compatibility variable.. this does not effect anything
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.
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 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.
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
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)
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.
float ** readribosum(char *name)
Read a ribosum or other user-defined scoring matrix.
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
float alifold(const char **strings, char *structure)
Compute MFE and according consensus structure of an alignment of sequences.
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 ...
float alipf_fold_par(const char **sequences, char *structure, plist **pl, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)
float alipf_circ_fold(const char **sequences, char *structure, plist **pl)
double * export_ali_bppm(void)
Get a pointer to the base pair probability array.
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...
char * alipbacktrack(double *prob)
Sample a consensus secondary structure from the Boltzmann ensemble according its probability .
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition data_structures.h:203
this datastructure is used as input parameter in functions of PS_dot.h and others
Definition data_structures.h:48