1 \hypertarget{alifold_8h_source}{
2 \section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h}
6 \begin{footnotesize}\begin{alltt}
7 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_ALIFOLD\_H\_\_}
8 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_ALIFOLD\_H\_\_}
9 00003 \textcolor{preprocessor}{}
10 00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
12 00043 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv_fact};
13 00052 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc_fact};
15 00054 \textcolor{comment}{/*}
16 00055 \textcolor{comment}{##############################################}
17 00056 \textcolor{comment}{# MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #}
18 00057 \textcolor{comment}{##############################################}
19 00058 \textcolor{comment}{*/}
21 00066 \textcolor{keywordtype}{void} \hyperlink{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{update_alifold_params}(\textcolor{keywordtype}{void});
24 00086 \textcolor{keywordtype}{float} \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings,
25 00087 \textcolor{keywordtype}{char} *structure);
28 00100 \textcolor{keywordtype}{float} \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings,
29 00101 \textcolor{keywordtype}{char} *structure);
31 00109 \textcolor{keywordtype}{void} \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free_alifold_arrays}(\textcolor{keywordtype}{void});
33 00122 \textcolor{keywordtype}{int} \hyperlink{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{get_mpi}(\textcolor{keywordtype}{char} *Alseq[],
34 00123 \textcolor{keywordtype}{int} n\_seq,
35 00124 \textcolor{keywordtype}{int} length,
36 00125 \textcolor{keywordtype}{int} *mini);
38 00133 \textcolor{keywordtype}{float} **\hyperlink{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{readribosum}(\textcolor{keywordtype}{char} *name);
40 00148 \textcolor{keywordtype}{float} \hyperlink{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{energy_of_alistruct}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
41 00149 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
42 00150 \textcolor{keywordtype}{int} n\_seq,
43 00151 \textcolor{keywordtype}{float} *energy);
45 00153 \textcolor{keywordtype}{float} energy\_of\_ali\_gquad\_structure(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
46 00154 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
47 00155 \textcolor{keywordtype}{int} n\_seq,
48 00156 \textcolor{keywordtype}{float} *energy);
50 00158 \textcolor{comment}{/*}
51 00159 \textcolor{comment}{#############################################################}
52 00160 \textcolor{comment}{# some helper functions that might be useful in the library #}
53 00161 \textcolor{comment}{#############################################################}
54 00162 \textcolor{comment}{*/}
56 00180 \textcolor{keywordtype}{void} \hyperlink{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{encode_ali_sequence}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
57 00181 \textcolor{keywordtype}{short} *S,
58 00182 \textcolor{keywordtype}{short} *s5,
59 00183 \textcolor{keywordtype}{short} *s3,
60 00184 \textcolor{keywordtype}{char} *ss,
61 00185 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} *as,
62 00186 \textcolor{keywordtype}{int} circ);
64 00205 \textcolor{keywordtype}{void} \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc_sequence_arrays}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
65 00206 \textcolor{keywordtype}{short} ***S,
66 00207 \textcolor{keywordtype}{short} ***S5,
67 00208 \textcolor{keywordtype}{short} ***S3,
68 00209 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} ***a2s,
69 00210 \textcolor{keywordtype}{char} ***Ss,
70 00211 \textcolor{keywordtype}{int} circ);
72 00229 \textcolor{keywordtype}{void} \hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free_sequence_arrays}( \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} n\_seq,
73 00230 \textcolor{keywordtype}{short} ***S,
74 00231 \textcolor{keywordtype}{short} ***S5,
75 00232 \textcolor{keywordtype}{short} ***S3,
76 00233 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} ***a2s,
77 00234 \textcolor{keywordtype}{char} ***Ss);
79 00236 \textcolor{comment}{/*}
80 00237 \textcolor{comment}{#############################################################}
81 00238 \textcolor{comment}{# PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #}
82 00239 \textcolor{comment}{#############################################################}
83 00240 \textcolor{comment}{*/}
86 00265 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf_fold_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
87 00266 \textcolor{keywordtype}{char} *structure,
88 00267 \hyperlink{structplist}{plist} **pl,
89 00268 \hyperlink{structpf__paramT}{pf_paramT} *parameters,
90 00269 \textcolor{keywordtype}{int} calculate\_bppm,
91 00270 \textcolor{keywordtype}{int} is\_constrained,
92 00271 \textcolor{keywordtype}{int} is\_circular);
94 00289 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf_fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
95 00290 \textcolor{keywordtype}{char} *structure,
96 00291 \hyperlink{structplist}{plist} **pl);
98 00303 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf_circ_fold}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
99 00304 \textcolor{keywordtype}{char} *structure,
100 00305 \hyperlink{structplist}{plist} **pl);
103 00319 FLT\_OR\_DBL *\hyperlink{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}{export_ali_bppm}(\textcolor{keywordtype}{void});
105 00327 \textcolor{keywordtype}{void} free\_alipf\_arrays(\textcolor{keywordtype}{void});
107 00344 \textcolor{keywordtype}{char} *\hyperlink{group__consensus__stochbt_ga0df40248788f0fb17ebdc59d74116d1c}{alipbacktrack}(\textcolor{keywordtype}{double} *prob);
110 00367 \textcolor{keywordtype}{int} \hyperlink{group__consensus__fold_ga5349960075b1847720a2e9df021e2675}{get_alipf_arrays}(\textcolor{keywordtype}{short} ***S\_p,
111 00368 \textcolor{keywordtype}{short} ***S5\_p,
112 00369 \textcolor{keywordtype}{short} ***S3\_p,
113 00370 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} ***a2s\_p,
114 00371 \textcolor{keywordtype}{char} ***Ss\_p,
115 00372 FLT\_OR\_DBL **qb\_p,
116 00373 FLT\_OR\_DBL **qm\_p,
117 00374 FLT\_OR\_DBL **q1k\_p,
118 00375 FLT\_OR\_DBL **qln\_p,
119 00376 \textcolor{keywordtype}{short} **pscore);
121 00378 \textcolor{preprocessor}{#endif}
122 \end{alltt}\end{footnotesize}