\hypertarget{fold_8h_source}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h}
}


\begin{footnotesize}\begin{alltt}
00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_FOLD\_H\_\_}
00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_FOLD\_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}{}
00061 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{logML};
00062 
00064 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{uniq_ML};
00065 
00067 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut_point};
00068 
00073 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos_debug};
00074 
00075 
00119 \textcolor{keywordtype}{float} \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
00120                 \textcolor{keywordtype}{char} *structure,
00121                 \hyperlink{structparamT}{paramT} *parameters,
00122                 \textcolor{keywordtype}{int} is\_constrained,
00123                 \textcolor{keywordtype}{int} is\_circular);
00124 
00143 \textcolor{keywordtype}{float} \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
00144             \textcolor{keywordtype}{char} *structure);
00145 
00164 \textcolor{keywordtype}{float} \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
00165                 \textcolor{keywordtype}{char} *structure);
00166 
00167 
00195 \textcolor{keywordtype}{float} \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy_of_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00196                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
00197                           \textcolor{keywordtype}{int} verbosity\_level);
00198 
00214 \textcolor{keywordtype}{float} \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy_of_struct_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00215                             \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
00216                             \hyperlink{structparamT}{paramT} *parameters,
00217                             \textcolor{keywordtype}{int} verbosity\_level);
00218 
00237 \textcolor{keywordtype}{float} \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy_of_circ_structure}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00238                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
00239                                 \textcolor{keywordtype}{int} verbosity\_level);
00240 
00256 \textcolor{keywordtype}{float} \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy_of_circ_struct_par}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00257                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
00258                                 \hyperlink{structparamT}{paramT} *parameters,
00259                                 \textcolor{keywordtype}{int} verbosity\_level);
00260 
00261 
00262 \textcolor{keywordtype}{float} energy\_of\_gquad\_structure(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00263                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
00264                                 \textcolor{keywordtype}{int} verbosity\_level);
00265 
00286 \textcolor{keywordtype}{int} \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy_of_structure_pt}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00287                             \textcolor{keywordtype}{short} *ptable,
00288                             \textcolor{keywordtype}{short} *s,
00289                             \textcolor{keywordtype}{short} *s1,
00290                             \textcolor{keywordtype}{int} verbosity\_level);
00291 
00309 \textcolor{keywordtype}{int} \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy_of_struct_pt_par}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00310                             \textcolor{keywordtype}{short} *ptable,
00311                             \textcolor{keywordtype}{short} *s,
00312                             \textcolor{keywordtype}{short} *s1,
00313                             \hyperlink{structparamT}{paramT} *parameters,
00314                             \textcolor{keywordtype}{int} verbosity\_level);
00315 
00322 \textcolor{keywordtype}{void}  \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free_arrays}(\textcolor{keywordtype}{void});
00323 
00324 
00330 \textcolor{keywordtype}{void}  \hyperlink{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{parenthesis_structure}(\textcolor{keywordtype}{char} *structure,
00331                             \hyperlink{structbondT}{bondT} *bp,
00332                             \textcolor{keywordtype}{int} length);
00333 
00340 \textcolor{keywordtype}{void} \hyperlink{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{parenthesis_zuker}( \textcolor{keywordtype}{char} *structure,
00341                         \hyperlink{structbondT}{bondT} *bp,
00342                         \textcolor{keywordtype}{int} length);
00343 
00344 \textcolor{keywordtype}{void} letter\_structure(\textcolor{keywordtype}{char} *structure,
00345                       \hyperlink{structbondT}{bondT} *bp,
00346                       \textcolor{keywordtype}{int} length);
00347 
00348 
00354 \textcolor{keywordtype}{void}  \hyperlink{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{update_fold_params}(\textcolor{keywordtype}{void});
00355 
00361 \textcolor{keywordtype}{void} update\_fold\_params\_par(\hyperlink{structparamT}{paramT} *parameters);
00362 
00368 \textcolor{keywordtype}{char}  *backtrack\_fold\_from\_pair(\textcolor{keywordtype}{char} *sequence,
00369                                 \textcolor{keywordtype}{int} i,
00370                                 \textcolor{keywordtype}{int} j);
00371 
00385 \textcolor{keywordtype}{float} \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy_of_move}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00386                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
00387                       \textcolor{keywordtype}{int} m1,
00388                       \textcolor{keywordtype}{int} m2);
00389 
00390 
00406 \textcolor{keywordtype}{int} \hyperlink{fold_8h_a49e0ee561be69faf0568213546f6a53f}{energy_of_move_pt}(\textcolor{keywordtype}{short} *pt,
00407                    \textcolor{keywordtype}{short} *s,
00408                    \textcolor{keywordtype}{short} *s1,
00409                    \textcolor{keywordtype}{int} m1,
00410                    \textcolor{keywordtype}{int} m2);
00411 
00421 \textcolor{keywordtype}{int}   \hyperlink{fold_8h_a507d4fd93f4b398d793ba2402731388d}{loop_energy}(\textcolor{keywordtype}{short} *ptable,
00422                   \textcolor{keywordtype}{short} *s,
00423                   \textcolor{keywordtype}{short} *s1,
00424                   \textcolor{keywordtype}{int} i);
00425 
00431 \textcolor{keywordtype}{void} export\_fold\_arrays(\textcolor{keywordtype}{int} **f5\_p,
00432                         \textcolor{keywordtype}{int} **c\_p,
00433                         \textcolor{keywordtype}{int} **fML\_p,
00434                         \textcolor{keywordtype}{int} **fM1\_p,
00435                         \textcolor{keywordtype}{int} **indx\_p,
00436                         \textcolor{keywordtype}{char} **ptype\_p);
00437 
00443 \textcolor{keywordtype}{void} export\_fold\_arrays\_par(\textcolor{keywordtype}{int} **f5\_p,
00444                             \textcolor{keywordtype}{int} **c\_p,
00445                             \textcolor{keywordtype}{int} **fML\_p,
00446                             \textcolor{keywordtype}{int} **fM1\_p,
00447                             \textcolor{keywordtype}{int} **indx\_p,
00448                             \textcolor{keywordtype}{char} **ptype\_p,
00449                             \hyperlink{structparamT}{paramT} **P\_p);
00450 
00456 \textcolor{keywordtype}{void} export\_circfold\_arrays(\textcolor{keywordtype}{int} *Fc\_p,
00457                             \textcolor{keywordtype}{int} *FcH\_p,
00458                             \textcolor{keywordtype}{int} *FcI\_p,
00459                             \textcolor{keywordtype}{int} *FcM\_p,
00460                             \textcolor{keywordtype}{int} **fM2\_p,
00461                             \textcolor{keywordtype}{int} **f5\_p,
00462                             \textcolor{keywordtype}{int} **c\_p,
00463                             \textcolor{keywordtype}{int} **fML\_p,
00464                             \textcolor{keywordtype}{int} **fM1\_p,
00465                             \textcolor{keywordtype}{int} **indx\_p,
00466                             \textcolor{keywordtype}{char} **ptype\_p);
00467 
00473 \textcolor{keywordtype}{void} export\_circfold\_arrays\_par(\textcolor{keywordtype}{int} *Fc\_p,
00474                                 \textcolor{keywordtype}{int} *FcH\_p,
00475                                 \textcolor{keywordtype}{int} *FcI\_p,
00476                                 \textcolor{keywordtype}{int} *FcM\_p,
00477                                 \textcolor{keywordtype}{int} **fM2\_p,
00478                                 \textcolor{keywordtype}{int} **f5\_p,
00479                                 \textcolor{keywordtype}{int} **c\_p,
00480                                 \textcolor{keywordtype}{int} **fML\_p,
00481                                 \textcolor{keywordtype}{int} **fM1\_p,
00482                                 \textcolor{keywordtype}{int} **indx\_p,
00483                                 \textcolor{keywordtype}{char} **ptype\_p,
00484                                 \hyperlink{structparamT}{paramT} **P\_p);
00485 
00486 
00504 \textcolor{keywordtype}{void} \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign_plist_from_db}(\hyperlink{structplist}{plist} **pl,
00505                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc,
00506                           \textcolor{keywordtype}{float} pr);
00507 
00508 \textcolor{comment}{/* finally moved the loop energy function declarations to this header...  */}
00509 \textcolor{comment}{/* BUT: The functions only exist for backward compatibility reasons!      */}
00510 \textcolor{comment}{/* You better include "loop\_energies.h" and call the functions:           */}
00511 \textcolor{comment}{/* E\_Hairpin() and E\_IntLoop() which are (almost) threadsafe as they get  */}
00512 \textcolor{comment}{/* a pointer to the energy parameter datastructure as additional argument */}
00513 
00518 DEPRECATED(\textcolor{keywordtype}{int} \hyperlink{fold_8h_a2163034a25c6115d894b199e97e03f6c}{LoopEnergy}(\textcolor{keywordtype}{int} n1,
00519                           \textcolor{keywordtype}{int} n2,
00520                           \textcolor{keywordtype}{int} type,
00521                           \textcolor{keywordtype}{int} type\_2,
00522                           \textcolor{keywordtype}{int} si1,
00523                           \textcolor{keywordtype}{int} sj1,
00524                           \textcolor{keywordtype}{int} sp1,
00525                           \textcolor{keywordtype}{int} sq1));
00526 
00531 DEPRECATED(\textcolor{keywordtype}{int} \hyperlink{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{HairpinE}(\textcolor{keywordtype}{int} size,
00532                         \textcolor{keywordtype}{int} type,
00533                         \textcolor{keywordtype}{int} si1,
00534                         \textcolor{keywordtype}{int} sj1,
00535                         \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}));
00536 
00542 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize_fold}(\textcolor{keywordtype}{int} length));
00543 
00558 DEPRECATED(\textcolor{keywordtype}{float} \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy_of_struct}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00559                                   \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure));
00560 
00577 DEPRECATED(\textcolor{keywordtype}{int} \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy_of_struct_pt}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00578                                     \textcolor{keywordtype}{short} *ptable,
00579                                     \textcolor{keywordtype}{short} *s,
00580                                     \textcolor{keywordtype}{short} *s1));
00581 
00596 DEPRECATED(\textcolor{keywordtype}{float} \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy_of_circ_struct}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
00597                                         \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure));
00598 
00599 \textcolor{preprocessor}{#endif}
\end{alltt}\end{footnotesize}
