\hypertarget{part__func_8h_source}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\-func.h}
}


\begin{footnotesize}\begin{alltt}
00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_H\_\_}
00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_H\_\_}
00003 \textcolor{preprocessor}{}
00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
00005 
00006 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))}
00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func}
00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
00011 \textcolor{preprocessor}{}
00012 
00041 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{st_back};
00042 
00043 \textcolor{comment}{/*}
00044 \textcolor{comment}{#################################################}
00045 \textcolor{comment}{# PARTITION FUNCTION COMPUTATION                #}
00046 \textcolor{comment}{#################################################}
00047 \textcolor{comment}{*/}
00048 
00087 \textcolor{keywordtype}{float}   \hyperlink{group__pf__fold_ga1839c61275760944b3a007c41d5c0823}{pf_fold_par}(  \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
00088                       \textcolor{keywordtype}{char} *structure,
00089                       \hyperlink{structpf__paramT}{pf_paramT} *parameters,
00090                       \textcolor{keywordtype}{int} calculate\_bppm,
00091                       \textcolor{keywordtype}{int} is\_constrained,
00092                       \textcolor{keywordtype}{int} is\_circular);
00093 
00133 \textcolor{keywordtype}{float}   \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf_fold}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
00134                 \textcolor{keywordtype}{char} *structure);
00135 
00161 \textcolor{keywordtype}{float}   \hyperlink{group__pf__fold_ga819ce5fca8984004ac81c4a3b04cb735}{pf_circ_fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
00162                       \textcolor{keywordtype}{char} *structure);
00163 
00173 \textcolor{keywordtype}{char}    *\hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack}(\textcolor{keywordtype}{char} *sequence);
00174 
00186 \textcolor{keywordtype}{char}    *\hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack_circ}(\textcolor{keywordtype}{char} *sequence);
00187 
00203 \textcolor{keywordtype}{void}  \hyperlink{group__pf__fold_gae73db3f49a94f0f72e067ecd12681dbd}{free_pf_arrays}(\textcolor{keywordtype}{void});
00204 
00214 \textcolor{keywordtype}{void}  \hyperlink{group__pf__fold_ga384e927890f9c034ff09fa66da102d28}{update_pf_params}(\textcolor{keywordtype}{int} length);
00215 
00222 \textcolor{keywordtype}{void} \hyperlink{group__pf__fold_ga0733527a94de3b79eee3c3c03c99c1bc}{update_pf_params_par}(\textcolor{keywordtype}{int} length, \hyperlink{structpf__paramT}{pf_paramT} *parameters);
00223 
00240 FLT\_OR\_DBL  *\hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export_bppm}(\textcolor{keywordtype}{void});
00241 
00242 \textcolor{comment}{/*}
00243 \textcolor{comment}{#################################################}
00244 \textcolor{comment}{# OTHER PARTITION FUNCTION RELATED DECLARATIONS #}
00245 \textcolor{comment}{#################################################}
00246 \textcolor{comment}{*/}
00247 
00265 \textcolor{keywordtype}{void}  \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign_plist_from_pr}( \hyperlink{structplist}{plist} **pl,
00266                             FLT\_OR\_DBL *probs,
00267                             \textcolor{keywordtype}{int} length,
00268                             \textcolor{keywordtype}{double} cutoff);
00269 
00270 \textcolor{comment}{/* this doesn't work if free\_pf\_arrays() is called before */}
00271 \textcolor{keywordtype}{void} assign\_plist\_gquad\_from\_pr(\hyperlink{structplist}{plist} **pl,
00272                                 \textcolor{keywordtype}{int} length,
00273                                 \textcolor{keywordtype}{double} cut\_off);
00274 
00275 \textcolor{keywordtype}{char} *get\_centroid\_struct\_gquad\_pr(\textcolor{keywordtype}{int} length,
00276                                   \textcolor{keywordtype}{double} *dist);
00277 
00293 \textcolor{keywordtype}{int} \hyperlink{group__pf__fold_ga18607e79e106cad827f482eedd2f632e}{get_pf_arrays}(\textcolor{keywordtype}{short} **S\_p,
00294                   \textcolor{keywordtype}{short} **S1\_p,
00295                   \textcolor{keywordtype}{char} **ptype\_p,
00296                   FLT\_OR\_DBL **qb\_p,
00297                   FLT\_OR\_DBL **qm\_p,
00298                   FLT\_OR\_DBL **q1k\_p,
00299                   FLT\_OR\_DBL **qln\_p);
00300 
00304 \textcolor{keywordtype}{double} \hyperlink{part__func_8h_a189e2a1ec6cc32c53ea72f7543b0441e}{get_subseq_F}(\textcolor{keywordtype}{int} i, \textcolor{keywordtype}{int} j);
00305 
00322 \textcolor{keywordtype}{char}  *\hyperlink{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}{get_centroid_struct_pl}(\textcolor{keywordtype}{int} length,
00323                               \textcolor{keywordtype}{double} *dist,
00324                               \hyperlink{structplist}{plist} *pl);
00325 
00342 \textcolor{keywordtype}{char}  *\hyperlink{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{get_centroid_struct_pr}(\textcolor{keywordtype}{int} length,
00343                               \textcolor{keywordtype}{double} *dist,
00344                               FLT\_OR\_DBL *pr);
00345 
00358 \textcolor{keywordtype}{double}  \hyperlink{group__pf__fold_ga79cbc375af65f11609feb6b055269e7d}{mean_bp_distance}(\textcolor{keywordtype}{int} length);
00359 
00377 \textcolor{keywordtype}{double}  \hyperlink{group__pf__fold_ga72d84525f0afd3a9d60d830a2f501fa5}{mean_bp_distance_pr}(\textcolor{keywordtype}{int} length,
00378                             FLT\_OR\_DBL *pr);
00379 
00383 \textcolor{keywordtype}{void}  \hyperlink{part__func_8h_a1f562d463c14d4703d9656056200eb38}{bppm_to_structure}(\textcolor{keywordtype}{char} *structure,
00384                         FLT\_OR\_DBL *pr,
00385                         \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length);
00386 
00387 \hyperlink{structplist}{plist} *stackProb(\textcolor{keywordtype}{double} cutoff);
00388 
00392 \textcolor{keywordtype}{char}    \hyperlink{part__func_8h_a49962ad6242b8c628de6ca16bb831c1d}{bppm_symbol}(\textcolor{keyword}{const} \textcolor{keywordtype}{float} *x);
00393 
00394 
00395 \textcolor{comment}{/*}
00396 \textcolor{comment}{#################################################}
00397 \textcolor{comment}{# DEPRECATED FUNCTIONS                          #}
00398 \textcolor{comment}{#################################################}
00399 \textcolor{comment}{*/}
00400 
00406 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{init_pf_fold}(\textcolor{keywordtype}{int} length));
00407 
00412 DEPRECATED(\textcolor{keywordtype}{char} *\hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid}(\textcolor{keywordtype}{int} length,
00413                           \textcolor{keywordtype}{double} *dist));     \textcolor{comment}{/* mean pair distance of ensemble *
      /}
00414 
00420 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{mean_bp_dist}(\textcolor{keywordtype}{int} length));
00421 
00425 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{expLoopEnergy}(\textcolor{keywordtype}{int} u1,
00426                                 \textcolor{keywordtype}{int} u2,
00427                                 \textcolor{keywordtype}{int} type,
00428                                 \textcolor{keywordtype}{int} type2,
00429                                 \textcolor{keywordtype}{short} si1,
00430                                 \textcolor{keywordtype}{short} sj1,
00431                                 \textcolor{keywordtype}{short} sp1,
00432                                 \textcolor{keywordtype}{short} sq1));
00433 
00437 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{expHairpinEnergy}( \textcolor{keywordtype}{int} u,
00438                                     \textcolor{keywordtype}{int} type,
00439                                     \textcolor{keywordtype}{short} si1,
00440                                     \textcolor{keywordtype}{short} sj1,
00441                                     \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}));
00442 
00443 \textcolor{preprocessor}{#endif}
\end{alltt}\end{footnotesize}
