binaries/src/ViennaRNA/doc/latex/alifold_8h_source.tex

   1 \hypertarget{alifold_8h}{\section{alifold.\-h}
   2 \label{alifold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/alifold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/alifold.\-h}}
   3 }
   4
   5 \begin{DoxyCode}
   6 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_ALIFOLD\_H\_\_}
   7 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_ALIFOLD\_H\_\_}
   8 00003 \textcolor{preprocessor}{}
   9 00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
  10 00005
  11 00043 \textcolor{keyword}{extern}  \textcolor{keywordtype}{double}  \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv\_fact};
  12 00052 \textcolor{keyword}{extern}  \textcolor{keywordtype}{double}  \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc\_fact};
  13 00053
  14 00054 \textcolor{comment}{/*}
  15 00055 \textcolor{comment}{##############################################}
  16 00056 \textcolor{comment}{# MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #}
  17 00057 \textcolor{comment}{##############################################}
  18 00058 \textcolor{comment}{*/}
  19 00059
  20 00066 \textcolor{keywordtype}{void} \hyperlink{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{update\_alifold\_params}(\textcolor{keywordtype}{void});
  21 00067
  22 00068
  23 00086 \textcolor{keywordtype}{float}  \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings,
  24 00087                 \textcolor{keywordtype}{char} *structure);
  25 00088
  26 00089
  27 00100 \textcolor{keywordtype}{float}  \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings,
  28 00101                     \textcolor{keywordtype}{char} *structure);
  29 00102
  30 00109 \textcolor{keywordtype}{void}    \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free\_alifold\_arrays}(\textcolor{keywordtype}{void});
  31 00110
  32 00122 \textcolor{keywordtype}{int} \hyperlink{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{get\_mpi}(\textcolor{keywordtype}{char} *Alseq[],
  33 00123             \textcolor{keywordtype}{int} n\_seq,
  34 00124             \textcolor{keywordtype}{int} length,
  35 00125             \textcolor{keywordtype}{int} *mini);
  36 00126
  37 00133 \textcolor{keywordtype}{float}   **\hyperlink{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{readribosum}(\textcolor{keywordtype}{char} *name);
  38 00134
  39 00148 \textcolor{keywordtype}{float}   \hyperlink{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{energy\_of\_alistruct}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
  40 00149                             \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
  41 00150                             \textcolor{keywordtype}{int} n\_seq,
  42 00151                             \textcolor{keywordtype}{float} *energy);
  43 00152
  44 00153 \textcolor{keywordtype}{float}   energy\_of\_ali\_gquad\_structure(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
  45 00154                                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
  46 00155                                       \textcolor{keywordtype}{int} n\_seq,
  47 00156                                       \textcolor{keywordtype}{float} *energy);
  48 00157
  49 00158 \textcolor{comment}{/*}
  50 00159 \textcolor{comment}{#############################################################}
  51 00160 \textcolor{comment}{# some helper functions that might be useful in the library #}
  52 00161 \textcolor{comment}{#############################################################}
  53 00162 \textcolor{comment}{*/}
  54 00163
  55 00180 \textcolor{keywordtype}{void} \hyperlink{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{encode\_ali\_sequence}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
  56 00181                           \textcolor{keywordtype}{short} *S,
  57 00182                           \textcolor{keywordtype}{short} *s5,
  58 00183                           \textcolor{keywordtype}{short} *s3,
  59 00184                           \textcolor{keywordtype}{char} *ss,
  60 00185                           \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} *as,
  61 00186                           \textcolor{keywordtype}{int} circ);
  62 00187
  63 00205 \textcolor{keywordtype}{void}  \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\_sequence\_arrays}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
  64 00206                             \textcolor{keywordtype}{short} ***S,
  65 00207                             \textcolor{keywordtype}{short} ***S5,
  66 00208                             \textcolor{keywordtype}{short} ***S3,
  67 00209                             \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} ***a2s,
  68 00210                             \textcolor{keywordtype}{char} ***Ss,
  69 00211                             \textcolor{keywordtype}{int} circ);
  70 00212
  71 00229 \textcolor{keywordtype}{void}  \hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free\_sequence\_arrays}( \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} n\_seq,
  72 00230                             \textcolor{keywordtype}{short} ***S,
  73 00231                             \textcolor{keywordtype}{short} ***S5,
  74 00232                             \textcolor{keywordtype}{short} ***S3,
  75 00233                             \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} ***a2s,
  76 00234                             \textcolor{keywordtype}{char} ***Ss);
  77 00235
  78 00236 \textcolor{comment}{/*}
  79 00237 \textcolor{comment}{#############################################################}
  80 00238 \textcolor{comment}{# PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #}
  81 00239 \textcolor{comment}{#############################################################}
  82 00240 \textcolor{comment}{*/}
  83 00241
  84 00242
  85 00265 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf\_fold\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
  86 00266                       \textcolor{keywordtype}{char} *structure,
  87 00267                       \hyperlink{structplist}{plist} **pl,
  88 00268                       \hyperlink{structpf__paramT}{pf\_paramT} *parameters,
  89 00269                       \textcolor{keywordtype}{int} calculate\_bppm,
  90 00270                       \textcolor{keywordtype}{int} is\_constrained,
  91 00271                       \textcolor{keywordtype}{int} is\_circular);
  92 00272
  93 00289 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\_fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
  94 00290                   \textcolor{keywordtype}{char} *structure,
  95 00291                   \hyperlink{structplist}{plist} **pl);
  96 00292
  97 00303 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\_circ\_fold}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
  98 00304                       \textcolor{keywordtype}{char} *structure,
  99 00305                       \hyperlink{structplist}{plist} **pl);
 100 00306
 101 00307
 102 00319 FLT\_OR\_DBL *\hyperlink{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{export\_ali\_bppm}(\textcolor{keywordtype}{void});
 103 00320
 104 00327 \textcolor{keywordtype}{void}  free\_alipf\_arrays(\textcolor{keywordtype}{void});
 105 00328
 106 00344 \textcolor{keywordtype}{char}  *\hyperlink{group__consensus__stochbt_ga0df40248788f0fb17ebdc59d74116d1c}{alipbacktrack}(\textcolor{keywordtype}{double} *prob);
 107 00345
 108 00346
 109 00367 \textcolor{keywordtype}{int} \hyperlink{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}{get\_alipf\_arrays}(\textcolor{keywordtype}{short} ***S\_p,
 110 00368          \textcolor{keywordtype}{short} ***S5\_p,
 111 00369          \textcolor{keywordtype}{short} ***S3\_p,
 112 00370          \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} ***a2s\_p,
 113 00371          \textcolor{keywordtype}{char} ***Ss\_p,
 114 00372          FLT\_OR\_DBL **qb\_p,
 115 00373          FLT\_OR\_DBL **qm\_p,
 116 00374          FLT\_OR\_DBL **q1k\_p,
 117 00375          FLT\_OR\_DBL **qln\_p,
 118 00376          \textcolor{keywordtype}{short} **pscore);
 119 00377
 120 00378 \textcolor{preprocessor}{#endif}
 121 \end{DoxyCode}