binaries/src/ViennaRNA/doc/latex/part__func__co_8h_source.tex

   1 \hypertarget{part__func__co_8h}{\section{part\-\_\-func\-\_\-co.\-h}
   2 \label{part__func__co_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-co.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-co.\-h}}
   3 }
   4
   5 \begin{DoxyCode}
   6 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_CO\_H\_\_}
   7 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_CO\_H\_\_}
   8 00003 \textcolor{preprocessor}{}
   9 00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
  10 00005
  11 00006 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
  12 00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))}
  13 00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
  14 00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func}
  15 00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  16 00011 \textcolor{preprocessor}{}
  17 00055 \textcolor{keyword}{extern} \textcolor{keywordtype}{int}    \hyperlink{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}{mirnatog};
  18 00056
  19 00060 \textcolor{keyword}{extern} \textcolor{keywordtype}{double} \hyperlink{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{F\_monomer}[2];
  20 00061
  21 00080 \hyperlink{structcofoldF}{cofoldF} \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\_pf\_fold}( \textcolor{keywordtype}{char} *sequence,
  22 00081                     \textcolor{keywordtype}{char} *structure);
  23 00082
  24 00100 \hyperlink{structcofoldF}{cofoldF} \hyperlink{group__pf__cofold_gabd873b450832ab5f21101fc5ab354d21}{co\_pf\_fold\_par}( \textcolor{keywordtype}{char} *sequence,
  25 00101                         \textcolor{keywordtype}{char} *structure,
  26 00102                         \hyperlink{structpf__paramT}{pf\_paramT} *parameters,
  27 00103                         \textcolor{keywordtype}{int} calculate\_bppm,
  28 00104                         \textcolor{keywordtype}{int} is\_constrained);
  29 00105
  30 00115 FLT\_OR\_DBL *\hyperlink{group__pf__cofold_ga11f0252c1d2c4697253ff4b5bd392d3c}{export\_co\_bppm}(\textcolor{keywordtype}{void});
  31 00116
  32 00120 \textcolor{keywordtype}{void}    \hyperlink{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{free\_co\_pf\_arrays}(\textcolor{keywordtype}{void});
  33 00121
  34 00136 \textcolor{keywordtype}{void}    \hyperlink{group__pf__cofold_ga6e0f36c1f9b7d9dd4bfbad914c1119e5}{update\_co\_pf\_params}(\textcolor{keywordtype}{int} length);
  35 00137
  36 00157 \textcolor{keywordtype}{void}    \hyperlink{group__pf__cofold_ga117d880df45bef444d5e2785ffa40a53}{update\_co\_pf\_params\_par}(\textcolor{keywordtype}{int} length,
  37 00158                                 \hyperlink{structpf__paramT}{pf\_paramT} *parameters);
  38 00159
  39 00177 \textcolor{keywordtype}{void}    \hyperlink{group__pf__cofold_ga15ae04ac5ab84e876dcf0093120cb617}{compute\_probabilities}(\textcolor{keywordtype}{double} FAB,
  40 00178                               \textcolor{keywordtype}{double} FEA,
  41 00179                               \textcolor{keywordtype}{double} FEB,
  42 00180                               \textcolor{keyword}{struct} \hyperlink{structplist}{plist}  *prAB,
  43 00181                               \textcolor{keyword}{struct} \hyperlink{structplist}{plist}  *prA,
  44 00182                               \textcolor{keyword}{struct} \hyperlink{structplist}{plist}  *prB,
  45 00183                               \textcolor{keywordtype}{int} Alength);
  46 00184
  47 00203 \hyperlink{structConcEnt}{ConcEnt} *\hyperlink{group__pf__cofold_ga5545cb936ac4ff93c7d699d46e72e8c7}{get\_concentrations}(\textcolor{keywordtype}{double} FEAB,
  48 00204                             \textcolor{keywordtype}{double} FEAA,
  49 00205                             \textcolor{keywordtype}{double} FEBB,
  50 00206                             \textcolor{keywordtype}{double} FEA,
  51 00207                             \textcolor{keywordtype}{double} FEB,
  52 00208                             \textcolor{keywordtype}{double} *startconc);
  53 00209
  54 00210
  55 00215 \textcolor{comment}{/*}
  56 00216 \textcolor{comment}{#################################################}
  57 00217 \textcolor{comment}{# DEPRECATED FUNCTIONS                          #}
  58 00218 \textcolor{comment}{#################################################}
  59 00219 \textcolor{comment}{*/}
  60 00220
  61 00226 DEPRECATED(\hyperlink{structplist}{plist}  *\hyperlink{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{get\_plist}( \textcolor{keyword}{struct} \hyperlink{structplist}{plist} *pl,
  62 00227                               \textcolor{keywordtype}{int} length,
  63 00228                               \textcolor{keywordtype}{double} cut\_off));
  64 00233 DEPRECATED(\textcolor{keywordtype}{void}   \hyperlink{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{init\_co\_pf\_fold}(\textcolor{keywordtype}{int} length));
  65 00234
  66 00235 \textcolor{preprocessor}{#endif}
  67 \end{DoxyCode}