// global functions char* vrna_centroid ( vrna_fold_compound_t* vc, double* dist ) char* vrna_centroid_from_plist ( int length, double* dist, vrna_ep_t* pl ) char* vrna_centroid_from_probs ( int length, double* dist, FLT_OR_DBL* probs )
char* vrna_centroid ( vrna_fold_compound_t* vc, double* dist )
The centroid is the structure with the minimal average distance to all other structures
:math:` <d(S)> = sum_{(i,j) in S} (1-p_{ij}) + sum_{(i,j) notin S} p_{ij} `
Thus, the centroid is simply the structure containing all pairs with \(p_ij>0.5\) The distance of the centroid to the ensemble is written to the memory adressed by dist .
Parameters:
vc | The fold compound data structure |
dist | A pointer to the distance variable where the centroid distance will be written to |
Returns:
The centroid structure of the ensemble in dot-bracket notation
char* vrna_centroid_from_plist ( int length, double* dist, vrna_ep_t* pl )
This function is a threadsafe replacement for centroid() with a vrna_ep_t input
The centroid is the structure with the minimal average distance to all other structures
:math:` <d(S)> = sum_{(i,j) in S} (1-p_{ij}) + sum_{(i,j) notin S} p_{ij} `
Thus, the centroid is simply the structure containing all pairs with \(p_ij>0.5\) The distance of the centroid to the ensemble is written to the memory adressed by dist .
Parameters:
length | The length of the sequence |
dist | A pointer to the distance variable where the centroid distance will be written to |
pl | A pair list containing base pair probability information about the ensemble |
Returns:
The centroid structure of the ensemble in dot-bracket notation
char* vrna_centroid_from_probs ( int length, double* dist, FLT_OR_DBL* probs )
This function is a threadsafe replacement for centroid() with a probability array input
The centroid is the structure with the minimal average distance to all other structures
:math:` <d(S)> = sum_{(i,j) in S} (1-p_{ij}) + sum_{(i,j) notin S} p_{ij} `
Thus, the centroid is simply the structure containing all pairs with \(p_ij>0.5\) The distance of the centroid to the ensemble is written to the memory adressed by dist .
Parameters:
length | The length of the sequence |
dist | A pointer to the distance variable where the centroid distance will be written to |
probs | An upper triangular matrix containing base pair probabilities (access via iindx vrna_idx_row_wise() ) |
Returns:
The centroid structure of the ensemble in dot-bracket notation