1\hypertarget{io_2file__formats_8h_source}{}\doxysection{file\+\_\+formats.\+h} 2\label{io_2file__formats_8h_source}\index{ViennaRNA/io/file\_formats.h@{ViennaRNA/io/file\_formats.h}} 3 4\begin{DoxyCode}{0} 5\DoxyCodeLine{00001 \textcolor{preprocessor}{\#ifndef VIENNA\_RNA\_PACKAGE\_FILE\_FORMATS\_H}} 6\DoxyCodeLine{00002 \textcolor{preprocessor}{\#define VIENNA\_RNA\_PACKAGE\_FILE\_FORMATS\_H}} 7\DoxyCodeLine{00003 } 8\DoxyCodeLine{00004 \textcolor{preprocessor}{\#ifdef VRNA\_WARN\_DEPRECATED}} 9\DoxyCodeLine{00005 \textcolor{preprocessor}{\# if defined(\_\_clang\_\_)}} 10\DoxyCodeLine{00006 \textcolor{preprocessor}{\# define DEPRECATED(func, msg) func \_\_attribute\_\_ ((deprecated("{}"{}}, msg)))} 11\DoxyCodeLine{00007 \textcolor{preprocessor}{\# elif defined(\_\_GNUC\_\_)}} 12\DoxyCodeLine{00008 \textcolor{preprocessor}{\# define DEPRECATED(func, msg) func \_\_attribute\_\_ ((deprecated(msg)))}} 13\DoxyCodeLine{00009 \textcolor{preprocessor}{\# else}} 14\DoxyCodeLine{00010 \textcolor{preprocessor}{\# define DEPRECATED(func, msg) func}} 15\DoxyCodeLine{00011 \textcolor{preprocessor}{\# endif}} 16\DoxyCodeLine{00012 \textcolor{preprocessor}{\#else}} 17\DoxyCodeLine{00013 \textcolor{preprocessor}{\# define DEPRECATED(func, msg) func}} 18\DoxyCodeLine{00014 \textcolor{preprocessor}{\#endif}} 19\DoxyCodeLine{00015 } 20\DoxyCodeLine{00028 \textcolor{preprocessor}{\#include <stdio.h>}} 21\DoxyCodeLine{00029 } 22\DoxyCodeLine{00030 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{datastructures_2basic_8h}{ViennaRNA/datastructures/basic.h}}>}} 23\DoxyCodeLine{00031 } 24\DoxyCodeLine{00040 \textcolor{keywordtype}{void}} 25\DoxyCodeLine{\Hypertarget{io_2file__formats_8h_source_l00041}\mbox{\hyperlink{group__file__formats_gaaface7db12fadc3d271641c4515ab6e4}{00041}} \mbox{\hyperlink{group__file__formats_gaaface7db12fadc3d271641c4515ab6e4}{vrna\_file\_helixlist}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq,} 26\DoxyCodeLine{00042 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *db,} 27\DoxyCodeLine{00043 \textcolor{keywordtype}{float} energy,} 28\DoxyCodeLine{00044 FILE *file);} 29\DoxyCodeLine{00045 } 30\DoxyCodeLine{00046 } 31\DoxyCodeLine{00070 \textcolor{keywordtype}{void}} 32\DoxyCodeLine{\Hypertarget{io_2file__formats_8h_source_l00071}\mbox{\hyperlink{group__file__formats_gab69682373ccca1e0e28cc967eec07745}{00071}} \mbox{\hyperlink{group__file__formats_gab69682373ccca1e0e28cc967eec07745}{vrna\_file\_connect}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq,} 33\DoxyCodeLine{00072 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *db,} 34\DoxyCodeLine{00073 \textcolor{keywordtype}{float} energy,} 35\DoxyCodeLine{00074 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *identifier,} 36\DoxyCodeLine{00075 FILE *file);} 37\DoxyCodeLine{00076 } 38\DoxyCodeLine{00077 } 39\DoxyCodeLine{00085 \textcolor{keywordtype}{void}} 40\DoxyCodeLine{\Hypertarget{io_2file__formats_8h_source_l00086}\mbox{\hyperlink{group__file__formats_ga9b462e6f202594af5d3fa56e280d633f}{00086}} \mbox{\hyperlink{group__file__formats_ga9b462e6f202594af5d3fa56e280d633f}{vrna\_file\_bpseq}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq,} 41\DoxyCodeLine{00087 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *db,} 42\DoxyCodeLine{00088 FILE *file);} 43\DoxyCodeLine{00089 } 44\DoxyCodeLine{00090 } 45\DoxyCodeLine{00091 \textcolor{preprocessor}{\#if VRNA\_WITH\_JSON\_SUPPORT}} 46\DoxyCodeLine{00092 } 47\DoxyCodeLine{00102 \textcolor{keywordtype}{void}} 48\DoxyCodeLine{\Hypertarget{io_2file__formats_8h_source_l00103}\mbox{\hyperlink{group__file__formats_ga31f4a6c2ea1495a6e4f9eb45a9f6193d}{00103}} \mbox{\hyperlink{group__file__formats_ga31f4a6c2ea1495a6e4f9eb45a9f6193d}{vrna\_file\_json}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq,} 49\DoxyCodeLine{00104 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *db,} 50\DoxyCodeLine{00105 \textcolor{keywordtype}{double} energy,} 51\DoxyCodeLine{00106 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *identifier,} 52\DoxyCodeLine{00107 FILE *file);} 53\DoxyCodeLine{00108 } 54\DoxyCodeLine{00109 } 55\DoxyCodeLine{00110 \textcolor{preprocessor}{\#endif}} 56\DoxyCodeLine{00111 } 57\DoxyCodeLine{\Hypertarget{io_2file__formats_8h_source_l00121}\mbox{\hyperlink{group__file__formats_gabec89c09874528c6cb73140a4c3d86d7}{00121}} \textcolor{preprocessor}{\#define VRNA\_OPTION\_MULTILINE 32U}} 58\DoxyCodeLine{\Hypertarget{io_2file__formats_8h_source_l00126}\mbox{\hyperlink{group__file__formats_ga7d725ef525b29891abef3f1ed42599a4}{00126}} \textcolor{preprocessor}{\#define VRNA\_CONSTRAINT\_MULTILINE 32U}} 59\DoxyCodeLine{00127 } 60\DoxyCodeLine{00193 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}} 61\DoxyCodeLine{\Hypertarget{io_2file__formats_8h_source_l00194}\mbox{\hyperlink{group__file__formats_ga8cfb7e271efc9e1f34640acb85475639}{00194}} \mbox{\hyperlink{group__file__formats_ga8cfb7e271efc9e1f34640acb85475639}{vrna\_file\_fasta\_read\_record}}(\textcolor{keywordtype}{char} **header,} 62\DoxyCodeLine{00195 \textcolor{keywordtype}{char} **sequence,} 63\DoxyCodeLine{00196 \textcolor{keywordtype}{char} ***rest,} 64\DoxyCodeLine{00197 FILE *file,} 65\DoxyCodeLine{00198 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options);} 66\DoxyCodeLine{00199 } 67\DoxyCodeLine{00200 } 68\DoxyCodeLine{00217 \textcolor{keywordtype}{char} *} 69\DoxyCodeLine{\Hypertarget{io_2file__formats_8h_source_l00218}\mbox{\hyperlink{group__file__formats_gad37cbb63a05eed63ba25c91628409be0}{00218}} \mbox{\hyperlink{group__file__formats_gad37cbb63a05eed63ba25c91628409be0}{vrna\_extract\_record\_rest\_structure}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **lines,} 70\DoxyCodeLine{00219 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length,} 71\DoxyCodeLine{00220 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option);} 72\DoxyCodeLine{00221 } 73\DoxyCodeLine{00222 } 74\DoxyCodeLine{00235 \textcolor{keywordtype}{int}} 75\DoxyCodeLine{\Hypertarget{io_2file__formats_8h_source_l00236}\mbox{\hyperlink{group__file__formats_ga646ebf45450a69a7f2533f9ecd283a32}{00236}} \mbox{\hyperlink{group__file__formats_ga646ebf45450a69a7f2533f9ecd283a32}{vrna\_file\_SHAPE\_read}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *file\_name,} 76\DoxyCodeLine{00237 \textcolor{keywordtype}{int} length,} 77\DoxyCodeLine{00238 \textcolor{keywordtype}{double} default\_value,} 78\DoxyCodeLine{00239 \textcolor{keywordtype}{char} *sequence,} 79\DoxyCodeLine{00240 \textcolor{keywordtype}{double} *values);} 80\DoxyCodeLine{00241 } 81\DoxyCodeLine{00242 } 82\DoxyCodeLine{00243 \textcolor{preprocessor}{\#ifndef VRNA\_DISABLE\_BACKWARD\_COMPATIBILITY}} 83\DoxyCodeLine{00244 } 84\DoxyCodeLine{00261 DEPRECATED(\textcolor{keywordtype}{void} \mbox{\hyperlink{group__file__formats_ga55a9ae6dfeecc1b3f0c2acf6fa796c15}{vrna\_extract\_record\_rest\_constraint}}(\textcolor{keywordtype}{char} **cstruc,} 85\DoxyCodeLine{00262 \textcolor{keyword}{const} \textcolor{keywordtype}{char} **lines,} 86\DoxyCodeLine{00263 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option),} 87\DoxyCodeLine{\Hypertarget{io_2file__formats_8h_source_l00264}\mbox{\hyperlink{group__file__formats_ga55a9ae6dfeecc1b3f0c2acf6fa796c15}{00264}} \textcolor{stringliteral}{"{}This function is obsolete"{}});} 88\DoxyCodeLine{00265 } 89\DoxyCodeLine{00270 DEPRECATED(\textcolor{keywordtype}{char} *extract\_record\_rest\_structure(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **lines,} 90\DoxyCodeLine{00271 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length,} 91\DoxyCodeLine{00272 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option),} 92\DoxyCodeLine{00273 \textcolor{stringliteral}{"{}Use vrna\_extract\_record\_rest\_structure() instead"{}});} 93\DoxyCodeLine{00274 } 94\DoxyCodeLine{00281 DEPRECATED(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \mbox{\hyperlink{group__file__formats_gafd194a69af9d92b5b0412a7627ac1595}{read\_record}}(\textcolor{keywordtype}{char} **header,} 95\DoxyCodeLine{00282 \textcolor{keywordtype}{char} **sequence,} 96\DoxyCodeLine{00283 \textcolor{keywordtype}{char} ***rest,} 97\DoxyCodeLine{00284 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options),} 98\DoxyCodeLine{\Hypertarget{io_2file__formats_8h_source_l00285}\mbox{\hyperlink{group__file__formats_gafd194a69af9d92b5b0412a7627ac1595}{00285}} \textcolor{stringliteral}{"{}Use vrna\_file\_fasta\_read\_record() instead"{}});} 99\DoxyCodeLine{00286 } 100\DoxyCodeLine{00287 } 101\DoxyCodeLine{00288 DEPRECATED(\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} get\_multi\_input\_line(\textcolor{keywordtype}{char} **\textcolor{keywordtype}{string},} 102\DoxyCodeLine{00289 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options),} 103\DoxyCodeLine{00290 \textcolor{stringliteral}{"{}This function is obsolete"{}});} 104\DoxyCodeLine{00291 } 105\DoxyCodeLine{00292 \textcolor{preprocessor}{\#endif}} 106\DoxyCodeLine{00293 } 107\DoxyCodeLine{00298 \textcolor{preprocessor}{\#endif}} 108 109\end{DoxyCode} 110