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vrna_ep_t * | vrna_pfl_fold (const char *sequence, int window_size, int max_bp_span, float cutoff) |
| Compute base pair probabilities using a sliding-window approach. More...
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void | vrna_pfl_fold_cb (const char *sequence, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data) |
| Compute base pair probabilities using a sliding-window approach (callback version) More...
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double ** | vrna_pfl_fold_up (const char *sequence, int ulength, int window_size, int max_bp_span) |
| Compute probability of contiguous unpaired segments. More...
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void | vrna_pfl_fold_up_cb (const char *sequence, int ulength, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data) |
| Compute probability of contiguous unpaired segments. More...
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void | vrna_probs_window (vrna_fold_compound_t *fc, int ulength, unsigned int options, vrna_probs_window_callback *cb, void *data) |
| Compute various equilibrium probabilities under a sliding window approach. More...
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void | update_pf_paramsLP (int length) |
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vrna_ep_t * | pfl_fold (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup) |
| Compute partition functions for locally stable secondary structures. More...
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vrna_ep_t * | pfl_fold_par (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup, vrna_exp_param_t *parameters) |
| Compute partition functions for locally stable secondary structures.
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void | putoutpU_prob (double **pU, int length, int ulength, FILE *fp, int energies) |
| Writes the unpaired probabilities (pU) or opening energies into a file. More...
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void | putoutpU_prob_bin (double **pU, int length, int ulength, FILE *fp, int energies) |
| Writes the unpaired probabilities (pU) or opening energies into a binary file. More...
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void | init_pf_foldLP (int length) |
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Partition function implementation for the Lfold algorithm.