RNAlib-2.4.14
LPfold.h
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1 #ifndef VIENNA_RNA_PACKAGE_LPFOLD_H
2 #define VIENNA_RNA_PACKAGE_LPFOLD_H
3 
4 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
5 
16 #include <stdio.h>
17 
18 #include <ViennaRNA/datastructures/basic.h>
19 #include <ViennaRNA/params/basic.h>
20 #include <ViennaRNA/part_func_window.h>
21 
22 #ifdef VRNA_WARN_DEPRECATED
23 # if defined(__clang__)
24 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
25 # elif defined(__GNUC__)
26 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
27 # else
28 # define DEPRECATED(func, msg) func
29 # endif
30 #else
31 # define DEPRECATED(func, msg) func
32 #endif
33 
41 DEPRECATED(void update_pf_paramsLP(int length),
42 "This function is obsolete");
43 
44 
51 DEPRECATED(void update_pf_paramsLP_par(int length,
52  vrna_exp_param_t *parameters),
53 "Use the new API with vrna_folc_compound_t instead");
54 
55 
93 DEPRECATED(vrna_ep_t *pfl_fold(char *sequence,
94  int winSize,
95  int pairSize,
96  float cutoffb,
97  double **pU,
98  vrna_ep_t **dpp2,
99  FILE *pUfp,
100  FILE *spup),
101 "Use vrna_pfl_fold(), vrna_pfl_fold_cb(), vrna_pfl_fold_up(), or vrna_pfl_fold_up_cb() instead");
102 
103 
110 DEPRECATED(vrna_ep_t *pfl_fold_par(char *sequence,
111  int winSize,
112  int pairSize,
113  float cutoffb,
114  double **pU,
115  vrna_ep_t **dpp2,
116  FILE *pUfp,
117  FILE *spup,
118  vrna_exp_param_t *parameters),
119 "Use the new API and vrna_probs_window() instead");
120 
121 
122 DEPRECATED(void putoutpU_prob_par(double **pU,
123  int length,
124  int ulength,
125  FILE *fp,
126  int energies,
127  vrna_exp_param_t *parameters),
128 "");
129 
130 
145 DEPRECATED(void putoutpU_prob(double **pU,
146  int length,
147  int ulength,
148  FILE *fp,
149  int energies),
150 "");
151 
152 
153 DEPRECATED(void putoutpU_prob_bin_par(double **pU,
154  int length,
155  int ulength,
156  FILE *fp,
157  int energies,
158  vrna_exp_param_t *parameters),
159 "");
160 
161 
176 DEPRECATED(void putoutpU_prob_bin(double **pU,
177  int length,
178  int ulength,
179  FILE *fp,
180  int energies),
181 "");
182 
183 
189 DEPRECATED(void init_pf_foldLP(int length),
190 "This function is obsolete");
191 
192 #endif
193 
194 #endif
update_pf_paramsLP
void update_pf_paramsLP(int length)
pfl_fold
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.
basic.h
Various data structures and pre-processor macros.
init_pf_foldLP
void init_pf_foldLP(int length)
vrna_exp_param_s
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:103
basic.h
Functions to deal with sets of energy parameters.
putoutpU_prob
void putoutpU_prob(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a file.
pfl_fold_par
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.
part_func_window.h
Partition function and equilibrium probability implementation for the sliding window algorithm...
putoutpU_prob_bin
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.
vrna_elem_prob_s
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:453