--- /dev/null
+\hypertarget{fold_8h}{\section{fold.\-h}
+\label{fold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.\-h}}
+}
+
+\begin{DoxyCode}
+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{DoxyCode}
git://source.jalview.org / jabaws.git / blobdiff