1 \hypertarget{snofold_8h_source}{
2 \section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/snofold.h}
6 \begin{footnotesize}\begin{alltt}
7 00001 \textcolor{comment}{/* function from fold.c */}
8 00002 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_SNOFOLD\_H\_\_}
9 00003 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_SNOFOLD\_H\_\_}
10 00004 \textcolor{preprocessor}{}
11 00005 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
13 00007 \textcolor{comment}{/* Normal fold */}
15 00012 \textcolor{keywordtype}{int} snofold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
16 00013 \textcolor{keywordtype}{char} *structure,
17 00014 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_assym,
18 00015 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold,
19 00016 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
20 00017 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
21 00018 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
22 00019 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem);
23 00024 \textcolor{keywordtype}{void} snofree\_arrays(\textcolor{keyword}{const} \textcolor{keywordtype}{int} length); \textcolor{comment}{/* free arrays for mfe folding */}
24 00025 \textcolor{keywordtype}{void} snoinitialize\_fold(\textcolor{keywordtype}{int} length); \textcolor{comment}{/* allocate arrays for folding */}
25 00026 \textcolor{keywordtype}{void} snoupdate\_fold\_params(\textcolor{keywordtype}{void}); \textcolor{comment}{/* recalculate parameters */}
26 00027 \textcolor{keywordtype}{int} snoloop\_energy(\textcolor{keywordtype}{short} *ptable,
27 00028 \textcolor{keywordtype}{short} *s,
28 00029 \textcolor{keywordtype}{short} *s1,
29 00030 \textcolor{keywordtype}{int} i);
30 00031 \textcolor{keywordtype}{void} snoexport\_fold\_arrays( \textcolor{keywordtype}{int} **indx\_p,
31 00032 \textcolor{keywordtype}{int} **mLoop\_p,
32 00033 \textcolor{keywordtype}{int} **cLoop,
33 00034 \hyperlink{structfolden}{folden} ***fold\_p,
34 00035 \hyperlink{structfolden}{folden} ***fold\_p\_XS);
35 00036 \textcolor{keywordtype}{char} * snobacktrack\_fold\_from\_pair( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
36 00037 \textcolor{keywordtype}{int} i,
37 00038 \textcolor{keywordtype}{int} j);
38 00039 \textcolor{comment}{/* alifold */}
39 00040 \textcolor{keywordtype}{float} alisnofold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings,
40 00041 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_assym,
41 00042 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
42 00043 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
43 00044 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
44 00045 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
45 00046 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem);
46 00047 \textcolor{keywordtype}{void} alisnofree\_arrays(\textcolor{keyword}{const} \textcolor{keywordtype}{int} length);
47 00048 \textcolor{keywordtype}{char} *alisnobacktrack\_fold\_from\_pair(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequence,
48 00049 \textcolor{keywordtype}{int} i,
49 00050 \textcolor{keywordtype}{int} j,
50 00051 \textcolor{keywordtype}{int} *cov);
51 00052 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv_fact} \textcolor{comment}{/* =1 */};
52 00053 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc_fact} \textcolor{comment}{/* =1 */};
54 00055 \textcolor{comment}{/* max number of mismatch >>>>>..(( )).>>>> */}
55 00056 \textcolor{preprocessor}{#define MISMATCH 3}
56 00057 \textcolor{preprocessor}{}
57 00058 \textcolor{preprocessor}{#endif}
58 \end{alltt}\end{footnotesize}