binaries/src/ViennaRNA/doc/latex/fold_8h_source.tex

   1 \hypertarget{fold_8h}{\section{fold.\-h}
   2 \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}}
   3 }
   4
   5 \begin{DoxyCode}
   6 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_FOLD\_H\_\_}
   7 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_FOLD\_H\_\_}
   8 00003 \textcolor{preprocessor}{}
   9 00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
  10 00005
  11 00006 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
  12 00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))}
  13 00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
  14 00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func}
  15 00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  16 00011 \textcolor{preprocessor}{}
  17 00061 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{logML};
  18 00062
  19 00064 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{uniq\_ML};
  20 00065
  21 00067 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\_point};
  22 00068
  23 00073 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\_debug};
  24 00074
  25 00075
  26 00119 \textcolor{keywordtype}{float} \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
  27 00120                 \textcolor{keywordtype}{char} *structure,
  28 00121                 \hyperlink{structparamT}{paramT} *parameters,
  29 00122                 \textcolor{keywordtype}{int} is\_constrained,
  30 00123                 \textcolor{keywordtype}{int} is\_circular);
  31 00124
  32 00143 \textcolor{keywordtype}{float} \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
  33 00144             \textcolor{keywordtype}{char} *structure);
  34 00145
  35 00164 \textcolor{keywordtype}{float} \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
  36 00165                 \textcolor{keywordtype}{char} *structure);
  37 00166
  38 00167
  39 00195 \textcolor{keywordtype}{float} \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\_of\_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
  40 00196                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
  41 00197                           \textcolor{keywordtype}{int} verbosity\_level);
  42 00198
  43 00214 \textcolor{keywordtype}{float} \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\_of\_struct\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
  44 00215                             \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
  45 00216                             \hyperlink{structparamT}{paramT} *parameters,
  46 00217                             \textcolor{keywordtype}{int} verbosity\_level);
  47 00218
  48 00237 \textcolor{keywordtype}{float} \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\_of\_circ\_structure}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
  49 00238                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
  50 00239                                 \textcolor{keywordtype}{int} verbosity\_level);
  51 00240
  52 00256 \textcolor{keywordtype}{float} \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\_of\_circ\_struct\_par}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
  53 00257                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
  54 00258                                 \hyperlink{structparamT}{paramT} *parameters,
  55 00259                                 \textcolor{keywordtype}{int} verbosity\_level);
  56 00260
  57 00261
  58 00262 \textcolor{keywordtype}{float} energy\_of\_gquad\_structure(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
  59 00263                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
  60 00264                                 \textcolor{keywordtype}{int} verbosity\_level);
  61 00265
  62 00286 \textcolor{keywordtype}{int} \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\_of\_structure\_pt}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
  63 00287                             \textcolor{keywordtype}{short} *ptable,
  64 00288                             \textcolor{keywordtype}{short} *s,
  65 00289                             \textcolor{keywordtype}{short} *s1,
  66 00290                             \textcolor{keywordtype}{int} verbosity\_level);
  67 00291
  68 00309 \textcolor{keywordtype}{int} \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\_of\_struct\_pt\_par}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
  69 00310                             \textcolor{keywordtype}{short} *ptable,
  70 00311                             \textcolor{keywordtype}{short} *s,
  71 00312                             \textcolor{keywordtype}{short} *s1,
  72 00313                             \hyperlink{structparamT}{paramT} *parameters,
  73 00314                             \textcolor{keywordtype}{int} verbosity\_level);
  74 00315
  75 00322 \textcolor{keywordtype}{void}  \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free\_arrays}(\textcolor{keywordtype}{void});
  76 00323
  77 00324
  78 00330 \textcolor{keywordtype}{void}  \hyperlink{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{parenthesis\_structure}(\textcolor{keywordtype}{char} *structure,
  79 00331                             \hyperlink{structbondT}{bondT} *bp,
  80 00332                             \textcolor{keywordtype}{int} length);
  81 00333
  82 00340 \textcolor{keywordtype}{void} \hyperlink{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{parenthesis\_zuker}( \textcolor{keywordtype}{char} *structure,
  83 00341                         \hyperlink{structbondT}{bondT} *bp,
  84 00342                         \textcolor{keywordtype}{int} length);
  85 00343
  86 00344 \textcolor{keywordtype}{void} letter\_structure(\textcolor{keywordtype}{char} *structure,
  87 00345                       \hyperlink{structbondT}{bondT} *bp,
  88 00346                       \textcolor{keywordtype}{int} length);
  89 00347
  90 00348
  91 00354 \textcolor{keywordtype}{void}  \hyperlink{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{update\_fold\_params}(\textcolor{keywordtype}{void});
  92 00355
  93 00361 \textcolor{keywordtype}{void} update\_fold\_params\_par(\hyperlink{structparamT}{paramT} *parameters);
  94 00362
  95 00368 \textcolor{keywordtype}{char}  *backtrack\_fold\_from\_pair(\textcolor{keywordtype}{char} *sequence,
  96 00369                                 \textcolor{keywordtype}{int} i,
  97 00370                                 \textcolor{keywordtype}{int} j);
  98 00371
  99 00385 \textcolor{keywordtype}{float} \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\_of\_move}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 100 00386                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
 101 00387                       \textcolor{keywordtype}{int} m1,
 102 00388                       \textcolor{keywordtype}{int} m2);
 103 00389
 104 00390
 105 00406 \textcolor{keywordtype}{int} \hyperlink{fold_8h_a49e0ee561be69faf0568213546f6a53f}{energy\_of\_move\_pt}(\textcolor{keywordtype}{short} *pt,
 106 00407                    \textcolor{keywordtype}{short} *s,
 107 00408                    \textcolor{keywordtype}{short} *s1,
 108 00409                    \textcolor{keywordtype}{int} m1,
 109 00410                    \textcolor{keywordtype}{int} m2);
 110 00411
 111 00421 \textcolor{keywordtype}{int}   \hyperlink{fold_8h_a507d4fd93f4b398d793ba2402731388d}{loop\_energy}(\textcolor{keywordtype}{short} *ptable,
 112 00422                   \textcolor{keywordtype}{short} *s,
 113 00423                   \textcolor{keywordtype}{short} *s1,
 114 00424                   \textcolor{keywordtype}{int} i);
 115 00425
 116 00431 \textcolor{keywordtype}{void} export\_fold\_arrays(\textcolor{keywordtype}{int} **f5\_p,
 117 00432                         \textcolor{keywordtype}{int} **c\_p,
 118 00433                         \textcolor{keywordtype}{int} **fML\_p,
 119 00434                         \textcolor{keywordtype}{int} **fM1\_p,
 120 00435                         \textcolor{keywordtype}{int} **indx\_p,
 121 00436                         \textcolor{keywordtype}{char} **ptype\_p);
 122 00437
 123 00443 \textcolor{keywordtype}{void} export\_fold\_arrays\_par(\textcolor{keywordtype}{int} **f5\_p,
 124 00444                             \textcolor{keywordtype}{int} **c\_p,
 125 00445                             \textcolor{keywordtype}{int} **fML\_p,
 126 00446                             \textcolor{keywordtype}{int} **fM1\_p,
 127 00447                             \textcolor{keywordtype}{int} **indx\_p,
 128 00448                             \textcolor{keywordtype}{char} **ptype\_p,
 129 00449                             \hyperlink{structparamT}{paramT} **P\_p);
 130 00450
 131 00456 \textcolor{keywordtype}{void} export\_circfold\_arrays(\textcolor{keywordtype}{int} *Fc\_p,
 132 00457                             \textcolor{keywordtype}{int} *FcH\_p,
 133 00458                             \textcolor{keywordtype}{int} *FcI\_p,
 134 00459                             \textcolor{keywordtype}{int} *FcM\_p,
 135 00460                             \textcolor{keywordtype}{int} **fM2\_p,
 136 00461                             \textcolor{keywordtype}{int} **f5\_p,
 137 00462                             \textcolor{keywordtype}{int} **c\_p,
 138 00463                             \textcolor{keywordtype}{int} **fML\_p,
 139 00464                             \textcolor{keywordtype}{int} **fM1\_p,
 140 00465                             \textcolor{keywordtype}{int} **indx\_p,
 141 00466                             \textcolor{keywordtype}{char} **ptype\_p);
 142 00467
 143 00473 \textcolor{keywordtype}{void} export\_circfold\_arrays\_par(\textcolor{keywordtype}{int} *Fc\_p,
 144 00474                                 \textcolor{keywordtype}{int} *FcH\_p,
 145 00475                                 \textcolor{keywordtype}{int} *FcI\_p,
 146 00476                                 \textcolor{keywordtype}{int} *FcM\_p,
 147 00477                                 \textcolor{keywordtype}{int} **fM2\_p,
 148 00478                                 \textcolor{keywordtype}{int} **f5\_p,
 149 00479                                 \textcolor{keywordtype}{int} **c\_p,
 150 00480                                 \textcolor{keywordtype}{int} **fML\_p,
 151 00481                                 \textcolor{keywordtype}{int} **fM1\_p,
 152 00482                                 \textcolor{keywordtype}{int} **indx\_p,
 153 00483                                 \textcolor{keywordtype}{char} **ptype\_p,
 154 00484                                 \hyperlink{structparamT}{paramT} **P\_p);
 155 00485
 156 00486
 157 00504 \textcolor{keywordtype}{void} \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign\_plist\_from\_db}(\hyperlink{structplist}{plist} **pl,
 158 00505                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc,
 159 00506                           \textcolor{keywordtype}{float} pr);
 160 00507
 161 00508 \textcolor{comment}{/* finally moved the loop energy function declarations to this header...  */}
 162 00509 \textcolor{comment}{/* BUT: The functions only exist for backward compatibility reasons!      */}
 163 00510 \textcolor{comment}{/* You better include "loop\_energies.h" and call the functions:           */}
 164 00511 \textcolor{comment}{/* E\_Hairpin() and E\_IntLoop() which are (almost) threadsafe as they get  */}
 165 00512 \textcolor{comment}{/* a pointer to the energy parameter datastructure as additional argument */}
 166 00513
 167 00518 DEPRECATED(\textcolor{keywordtype}{int} \hyperlink{fold_8h_a2163034a25c6115d894b199e97e03f6c}{LoopEnergy}(\textcolor{keywordtype}{int} n1,
 168 00519                           \textcolor{keywordtype}{int} n2,
 169 00520                           \textcolor{keywordtype}{int} type,
 170 00521                           \textcolor{keywordtype}{int} type\_2,
 171 00522                           \textcolor{keywordtype}{int} si1,
 172 00523                           \textcolor{keywordtype}{int} sj1,
 173 00524                           \textcolor{keywordtype}{int} sp1,
 174 00525                           \textcolor{keywordtype}{int} sq1));
 175 00526
 176 00531 DEPRECATED(\textcolor{keywordtype}{int} \hyperlink{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{HairpinE}(\textcolor{keywordtype}{int} size,
 177 00532                         \textcolor{keywordtype}{int} type,
 178 00533                         \textcolor{keywordtype}{int} si1,
 179 00534                         \textcolor{keywordtype}{int} sj1,
 180 00535                         \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}));
 181 00536
 182 00542 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize\_fold}(\textcolor{keywordtype}{int} length));
 183 00543
 184 00558 DEPRECATED(\textcolor{keywordtype}{float} \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\_of\_struct}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 185 00559                                   \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure));
 186 00560
 187 00577 DEPRECATED(\textcolor{keywordtype}{int} \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\_of\_struct\_pt}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 188 00578                                     \textcolor{keywordtype}{short} *ptable,
 189 00579                                     \textcolor{keywordtype}{short} *s,
 190 00580                                     \textcolor{keywordtype}{short} *s1));
 191 00581
 192 00596 DEPRECATED(\textcolor{keywordtype}{float} \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\_of\_circ\_struct}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 193 00597                                         \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure));
 194 00598
 195 00599 \textcolor{preprocessor}{#endif}
 196 \end{DoxyCode}