\hypertarget{alifold_8h_source}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h}
}


\begin{footnotesize}\begin{alltt}
00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_ALIFOLD\_H\_\_}
00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_ALIFOLD\_H\_\_}
00003 \textcolor{preprocessor}{}
00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
00005 
00043 \textcolor{keyword}{extern}  \textcolor{keywordtype}{double}  \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv_fact};
00052 \textcolor{keyword}{extern}  \textcolor{keywordtype}{double}  \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc_fact};
00053 
00054 \textcolor{comment}{/*}
00055 \textcolor{comment}{##############################################}
00056 \textcolor{comment}{# MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #}
00057 \textcolor{comment}{##############################################}
00058 \textcolor{comment}{*/}
00059 
00066 \textcolor{keywordtype}{void} \hyperlink{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{update_alifold_params}(\textcolor{keywordtype}{void});
00067 
00068 
00086 \textcolor{keywordtype}{float}  \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings,
00087                 \textcolor{keywordtype}{char} *structure);
00088 
00089 
00100 \textcolor{keywordtype}{float}  \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings,
00101                     \textcolor{keywordtype}{char} *structure);
00102 
00109 \textcolor{keywordtype}{void}    \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free_alifold_arrays}(\textcolor{keywordtype}{void});
00110 
00122 \textcolor{keywordtype}{int} \hyperlink{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{get_mpi}(\textcolor{keywordtype}{char} *Alseq[],
00123             \textcolor{keywordtype}{int} n\_seq,
00124             \textcolor{keywordtype}{int} length,
00125             \textcolor{keywordtype}{int} *mini);
00126 
00133 \textcolor{keywordtype}{float}   **\hyperlink{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{readribosum}(\textcolor{keywordtype}{char} *name);
00134 
00148 \textcolor{keywordtype}{float}   \hyperlink{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{energy_of_alistruct}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
00149                             \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
00150                             \textcolor{keywordtype}{int} n\_seq,
00151                             \textcolor{keywordtype}{float} *energy);
00152 
00153 \textcolor{keywordtype}{float}   energy\_of\_ali\_gquad\_structure(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
00154                                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
00155                                       \textcolor{keywordtype}{int} n\_seq,
00156                                       \textcolor{keywordtype}{float} *energy);
00157 
00158 \textcolor{comment}{/*}
00159 \textcolor{comment}{#############################################################}
00160 \textcolor{comment}{# some helper functions that might be useful in the library #}
00161 \textcolor{comment}{#############################################################}
00162 \textcolor{comment}{*/}
00163 
00180 \textcolor{keywordtype}{void} \hyperlink{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{encode_ali_sequence}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
00181                           \textcolor{keywordtype}{short} *S,
00182                           \textcolor{keywordtype}{short} *s5,
00183                           \textcolor{keywordtype}{short} *s3,
00184                           \textcolor{keywordtype}{char} *ss,
00185                           \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} *as,
00186                           \textcolor{keywordtype}{int} circ);
00187 
00205 \textcolor{keywordtype}{void}  \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc_sequence_arrays}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
00206                             \textcolor{keywordtype}{short} ***S,
00207                             \textcolor{keywordtype}{short} ***S5,
00208                             \textcolor{keywordtype}{short} ***S3,
00209                             \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} ***a2s,
00210                             \textcolor{keywordtype}{char} ***Ss,
00211                             \textcolor{keywordtype}{int} circ);
00212 
00229 \textcolor{keywordtype}{void}  \hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free_sequence_arrays}( \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} n\_seq,
00230                             \textcolor{keywordtype}{short} ***S,
00231                             \textcolor{keywordtype}{short} ***S5,
00232                             \textcolor{keywordtype}{short} ***S3,
00233                             \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} ***a2s,
00234                             \textcolor{keywordtype}{char} ***Ss);
00235 
00236 \textcolor{comment}{/*}
00237 \textcolor{comment}{#############################################################}
00238 \textcolor{comment}{# PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #}
00239 \textcolor{comment}{#############################################################}
00240 \textcolor{comment}{*/}
00241 
00242 
00265 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf_fold_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
00266                       \textcolor{keywordtype}{char} *structure,
00267                       \hyperlink{structplist}{plist} **pl,
00268                       \hyperlink{structpf__paramT}{pf_paramT} *parameters,
00269                       \textcolor{keywordtype}{int} calculate\_bppm,
00270                       \textcolor{keywordtype}{int} is\_constrained,
00271                       \textcolor{keywordtype}{int} is\_circular);
00272 
00289 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf_fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
00290                   \textcolor{keywordtype}{char} *structure,
00291                   \hyperlink{structplist}{plist} **pl);
00292 
00303 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf_circ_fold}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
00304                       \textcolor{keywordtype}{char} *structure,
00305                       \hyperlink{structplist}{plist} **pl);
00306 
00307 
00319 FLT\_OR\_DBL *\hyperlink{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}{export_ali_bppm}(\textcolor{keywordtype}{void});
00320 
00327 \textcolor{keywordtype}{void}  free\_alipf\_arrays(\textcolor{keywordtype}{void});
00328 
00344 \textcolor{keywordtype}{char}  *\hyperlink{group__consensus__stochbt_ga0df40248788f0fb17ebdc59d74116d1c}{alipbacktrack}(\textcolor{keywordtype}{double} *prob);
00345 
00346 
00367 \textcolor{keywordtype}{int} \hyperlink{group__consensus__fold_ga5349960075b1847720a2e9df021e2675}{get_alipf_arrays}(\textcolor{keywordtype}{short} ***S\_p,
00368          \textcolor{keywordtype}{short} ***S5\_p,
00369          \textcolor{keywordtype}{short} ***S3\_p,
00370          \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} ***a2s\_p,
00371          \textcolor{keywordtype}{char} ***Ss\_p,
00372          FLT\_OR\_DBL **qb\_p,
00373          FLT\_OR\_DBL **qm\_p,
00374          FLT\_OR\_DBL **q1k\_p,
00375          FLT\_OR\_DBL **qln\_p,
00376          \textcolor{keywordtype}{short} **pscore);
00377 
00378 \textcolor{preprocessor}{#endif}
\end{alltt}\end{footnotesize}
