binaries/src/ViennaRNA/doc/latex/snofold_8h_source.tex

   1 \hypertarget{snofold_8h}{\section{snofold.\-h}
   2 \label{snofold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/snofold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/snofold.\-h}}
   3 }
   4
   5 \begin{DoxyCode}
   6 00001 \textcolor{comment}{/* function from fold.c */}
   7 00002 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_SNOFOLD\_H\_\_}
   8 00003 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_SNOFOLD\_H\_\_}
   9 00004 \textcolor{preprocessor}{}
  10 00005 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
  11 00006
  12 00007 \textcolor{comment}{/* Normal fold */}
  13 00008
  14 00012 \textcolor{keywordtype}{int}  snofold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
  15 00013     \textcolor{keywordtype}{char} *structure,
  16 00014                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_assym,
  17 00015                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshold,
  18 00016                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
  19 00017                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
  20 00018                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
  21 00019                 \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem);
  22 00024 \textcolor{keywordtype}{void}   snofree\_arrays(\textcolor{keyword}{const} \textcolor{keywordtype}{int} length);  \textcolor{comment}{/* free arrays for mfe folding */}
  23 00025 \textcolor{keywordtype}{void}   snoinitialize\_fold(\textcolor{keywordtype}{int} length);    \textcolor{comment}{/* allocate arrays for folding */}
  24 00026 \textcolor{keywordtype}{void}   snoupdate\_fold\_params(\textcolor{keywordtype}{void});       \textcolor{comment}{/* recalculate parameters */}
  25 00027 \textcolor{keywordtype}{int}    snoloop\_energy(\textcolor{keywordtype}{short} *ptable,
  26 00028                       \textcolor{keywordtype}{short} *s,
  27 00029                       \textcolor{keywordtype}{short} *s1,
  28 00030                       \textcolor{keywordtype}{int} i);
  29 00031 \textcolor{keywordtype}{void}   snoexport\_fold\_arrays( \textcolor{keywordtype}{int} **indx\_p,
  30 00032                               \textcolor{keywordtype}{int} **mLoop\_p,
  31 00033                               \textcolor{keywordtype}{int} **cLoop,
  32 00034                               \hyperlink{structfolden}{folden} ***fold\_p,
  33 00035                               \hyperlink{structfolden}{folden} ***fold\_p\_XS);
  34 00036 \textcolor{keywordtype}{char} * snobacktrack\_fold\_from\_pair( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
  35 00037                                     \textcolor{keywordtype}{int} i,
  36 00038                                     \textcolor{keywordtype}{int} j);
  37 00039 \textcolor{comment}{/* alifold */}
  38 00040 \textcolor{keywordtype}{float} alisnofold( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings,
  39 00041                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_assym,
  40 00042                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} threshloop,
  41 00043                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} min\_s2,
  42 00044                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_s2,
  43 00045                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} half\_stem,
  44 00046                   \textcolor{keyword}{const} \textcolor{keywordtype}{int} max\_half\_stem);
  45 00047 \textcolor{keywordtype}{void}  alisnofree\_arrays(\textcolor{keyword}{const} \textcolor{keywordtype}{int} length);
  46 00048 \textcolor{keywordtype}{char}  *alisnobacktrack\_fold\_from\_pair(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequence,
  47 00049                                       \textcolor{keywordtype}{int} i,
  48 00050                                       \textcolor{keywordtype}{int} j,
  49 00051                                       \textcolor{keywordtype}{int} *cov);
  50 00052 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv\_fact} \textcolor{comment}{/* =1 */};
  51 00053 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc\_fact} \textcolor{comment}{/* =1 */};
  52 00054
  53 00055 \textcolor{comment}{/* max number of mismatch >>>>>..((   )).>>>> */}
  54 00056 \textcolor{preprocessor}{#define MISMATCH 3}
  55 00057 \textcolor{preprocessor}{}
  56 00058 \textcolor{preprocessor}{#endif}
  57 \end{DoxyCode}