RNAlib-2.5.1
LPfold.h
Go to the documentation of this file.
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
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
41DEPRECATED(void update_pf_paramsLP(int length),
42"This function is obsolete");
43
44
51DEPRECATED(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
93DEPRECATED(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
110DEPRECATED(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
122DEPRECATED(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
145DEPRECATED(void putoutpU_prob(double **pU,
146 int length,
147 int ulength,
148 FILE *fp,
149 int energies),
150"");
151
152
153DEPRECATED(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
176DEPRECATED(void putoutpU_prob_bin(double **pU,
177 int length,
178 int ulength,
179 FILE *fp,
180 int energies),
181"");
182
183
189DEPRECATED(void init_pf_foldLP(int length),
190"This function is obsolete");
191
192#endif
193
194#endif
void init_pf_foldLP(int length)
Various data structures and pre-processor macros.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition: basic.h:103
void putoutpU_prob(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a file.
void update_pf_paramsLP(int length)
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_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.
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.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:482
Functions to deal with sets of energy parameters.
Partition function and equilibrium probability implementation for the sliding window algorithm.