\hypertarget{snofold_8h_source}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/snofold.h}
}


\begin{footnotesize}\begin{alltt}
00001 \textcolor{comment}{/* function from fold.c */}
00002 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_SNOFOLD\_H\_\_}
00003 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_SNOFOLD\_H\_\_}
00004 \textcolor{preprocessor}{}
00005 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
00006 
00007 \textcolor{comment}{/* Normal fold */}
00008 
00012 \textcolor{keywordtype}{int}  snofold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
00013     \textcolor{keywordtype}{char} *structure,
00014                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_assym,
00015                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold, 
00016                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00017                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00018                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00019                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem);
00024 \textcolor{keywordtype}{void}   snofree\_arrays(\textcolor{keyword}{const} \textcolor{keywordtype}{int} length);  \textcolor{comment}{/* free arrays for mfe folding */}
00025 \textcolor{keywordtype}{void}   snoinitialize\_fold(\textcolor{keywordtype}{int} length);    \textcolor{comment}{/* allocate arrays for folding */}
00026 \textcolor{keywordtype}{void}   snoupdate\_fold\_params(\textcolor{keywordtype}{void});       \textcolor{comment}{/* recalculate parameters */}
00027 \textcolor{keywordtype}{int}    snoloop\_energy(\textcolor{keywordtype}{short} *ptable,
00028                       \textcolor{keywordtype}{short} *s,
00029                       \textcolor{keywordtype}{short} *s1,
00030                       \textcolor{keywordtype}{int} i);
00031 \textcolor{keywordtype}{void}   snoexport\_fold\_arrays( \textcolor{keywordtype}{int} **indx\_p,
00032                               \textcolor{keywordtype}{int} **mLoop\_p,
00033                               \textcolor{keywordtype}{int} **cLoop,
00034                               \hyperlink{structfolden}{folden} ***fold\_p,
00035                               \hyperlink{structfolden}{folden} ***fold\_p\_XS);
00036 \textcolor{keywordtype}{char} * snobacktrack\_fold\_from\_pair( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
00037                                     \textcolor{keywordtype}{int} i,
00038                                     \textcolor{keywordtype}{int} j);
00039 \textcolor{comment}{/* alifold */}
00040 \textcolor{keywordtype}{float} alisnofold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings,
00041                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_assym,
00042                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop, 
00043                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
00044                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
00045                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
00046                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem);
00047 \textcolor{keywordtype}{void}  alisnofree\_arrays(\textcolor{keyword}{const} \textcolor{keywordtype}{int} length);
00048 \textcolor{keywordtype}{char}  *alisnobacktrack\_fold\_from\_pair(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequence,
00049                                       \textcolor{keywordtype}{int} i,
00050                                       \textcolor{keywordtype}{int} j,
00051                                       \textcolor{keywordtype}{int} *cov);
00052 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv_fact} \textcolor{comment}{/* =1 */};
00053 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc_fact} \textcolor{comment}{/* =1 */};
00054 
00055 \textcolor{comment}{/* max number of mismatch >>>>>..((   )).>>>> */}
00056 \textcolor{preprocessor}{#define MISMATCH 3}
00057 \textcolor{preprocessor}{}
00058 \textcolor{preprocessor}{#endif}
\end{alltt}\end{footnotesize}
