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JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.
[jabaws.git] / binaries / src / ViennaRNA / doc / latex / fold_8h_source.tex
diff --git a/binaries/src/ViennaRNA/doc/latex/fold_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/fold_8h_source.tex
index 1d1fc89..34c8c47 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/fold_8h_source.tex
+++ b/binaries/src/ViennaRNA/doc/latex/fold_8h_source.tex
@@ -1,12 +1,13 @@
-\hypertarget{fold_8h}{\section{fold.\-h}
-\label{fold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.\-h}}
+\hypertarget{fold_8h_source}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h}
 }
 
-\begin{DoxyCode}
+
+\begin{footnotesize}\begin{alltt}
 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_FOLD\_H\_\_}
 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_FOLD\_H\_\_}
 00003 \textcolor{preprocessor}{}
-00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
+00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data_structures.h}"}
 00005 
 00006 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
 00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))}
@@ -16,14 +17,14 @@
 00011 \textcolor{preprocessor}{}
 00061 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{logML};
 00062 
-00064 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{uniq\_ML};
+00064 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{uniq_ML};
 00065 
-00067 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\_point};
+00067 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut_point};
 00068 
-00073 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\_debug};
+00073 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos_debug};
 00074 
 00075 
-00119 \textcolor{keywordtype}{float} \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
+00119 \textcolor{keywordtype}{float} \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
 00120                 \textcolor{keywordtype}{char} *structure,
 00121                 \hyperlink{structparamT}{paramT} *parameters,
 00122                 \textcolor{keywordtype}{int} is\_constrained,
@@ -36,20 +37,20 @@
 00165                 \textcolor{keywordtype}{char} *structure);
 00166 
 00167 
-00195 \textcolor{keywordtype}{float} \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\_of\_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00195 \textcolor{keywordtype}{float} \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy_of_structure}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 00196                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
 00197                           \textcolor{keywordtype}{int} verbosity\_level);
 00198 
-00214 \textcolor{keywordtype}{float} \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\_of\_struct\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00214 \textcolor{keywordtype}{float} \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy_of_struct_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 00215                             \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
 00216                             \hyperlink{structparamT}{paramT} *parameters,
 00217                             \textcolor{keywordtype}{int} verbosity\_level);
 00218 
-00237 \textcolor{keywordtype}{float} \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\_of\_circ\_structure}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00237 \textcolor{keywordtype}{float} \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy_of_circ_structure}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 00238                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
 00239                                 \textcolor{keywordtype}{int} verbosity\_level);
 00240 
-00256 \textcolor{keywordtype}{float} \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\_of\_circ\_struct\_par}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00256 \textcolor{keywordtype}{float} \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy_of_circ_struct_par}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 00257                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
 00258                                 \hyperlink{structparamT}{paramT} *parameters,
 00259                                 \textcolor{keywordtype}{int} verbosity\_level);
@@ -59,27 +60,27 @@
 00263                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
 00264                                 \textcolor{keywordtype}{int} verbosity\_level);
 00265 
-00286 \textcolor{keywordtype}{int} \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\_of\_structure\_pt}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00286 \textcolor{keywordtype}{int} \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy_of_structure_pt}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 00287                             \textcolor{keywordtype}{short} *ptable,
 00288                             \textcolor{keywordtype}{short} *s,
 00289                             \textcolor{keywordtype}{short} *s1,
 00290                             \textcolor{keywordtype}{int} verbosity\_level);
 00291 
-00309 \textcolor{keywordtype}{int} \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\_of\_struct\_pt\_par}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00309 \textcolor{keywordtype}{int} \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy_of_struct_pt_par}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 00310                             \textcolor{keywordtype}{short} *ptable,
 00311                             \textcolor{keywordtype}{short} *s,
 00312                             \textcolor{keywordtype}{short} *s1,
 00313                             \hyperlink{structparamT}{paramT} *parameters,
 00314                             \textcolor{keywordtype}{int} verbosity\_level);
 00315 
-00322 \textcolor{keywordtype}{void}  \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free\_arrays}(\textcolor{keywordtype}{void});
+00322 \textcolor{keywordtype}{void}  \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free_arrays}(\textcolor{keywordtype}{void});
 00323 
 00324 
-00330 \textcolor{keywordtype}{void}  \hyperlink{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{parenthesis\_structure}(\textcolor{keywordtype}{char} *structure,
+00330 \textcolor{keywordtype}{void}  \hyperlink{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{parenthesis_structure}(\textcolor{keywordtype}{char} *structure,
 00331                             \hyperlink{structbondT}{bondT} *bp,
 00332                             \textcolor{keywordtype}{int} length);
 00333 
-00340 \textcolor{keywordtype}{void} \hyperlink{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{parenthesis\_zuker}( \textcolor{keywordtype}{char} *structure,
+00340 \textcolor{keywordtype}{void} \hyperlink{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{parenthesis_zuker}( \textcolor{keywordtype}{char} *structure,
 00341                         \hyperlink{structbondT}{bondT} *bp,
 00342                         \textcolor{keywordtype}{int} length);
 00343 
@@ -88,7 +89,7 @@
 00346                       \textcolor{keywordtype}{int} length);
 00347 
 00348 
-00354 \textcolor{keywordtype}{void}  \hyperlink{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{update\_fold\_params}(\textcolor{keywordtype}{void});
+00354 \textcolor{keywordtype}{void}  \hyperlink{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{update_fold_params}(\textcolor{keywordtype}{void});
 00355 
 00361 \textcolor{keywordtype}{void} update\_fold\_params\_par(\hyperlink{structparamT}{paramT} *parameters);
 00362 
@@ -96,19 +97,19 @@
 00369                                 \textcolor{keywordtype}{int} i,
 00370                                 \textcolor{keywordtype}{int} j);
 00371 
-00385 \textcolor{keywordtype}{float} \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\_of\_move}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00385 \textcolor{keywordtype}{float} \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy_of_move}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 00386                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
 00387                       \textcolor{keywordtype}{int} m1,
 00388                       \textcolor{keywordtype}{int} m2);
 00389 
 00390 
-00406 \textcolor{keywordtype}{int} \hyperlink{fold_8h_a49e0ee561be69faf0568213546f6a53f}{energy\_of\_move\_pt}(\textcolor{keywordtype}{short} *pt,
+00406 \textcolor{keywordtype}{int} \hyperlink{fold_8h_a49e0ee561be69faf0568213546f6a53f}{energy_of_move_pt}(\textcolor{keywordtype}{short} *pt,
 00407                    \textcolor{keywordtype}{short} *s,
 00408                    \textcolor{keywordtype}{short} *s1,
 00409                    \textcolor{keywordtype}{int} m1,
 00410                    \textcolor{keywordtype}{int} m2);
 00411 
-00421 \textcolor{keywordtype}{int}   \hyperlink{fold_8h_a507d4fd93f4b398d793ba2402731388d}{loop\_energy}(\textcolor{keywordtype}{short} *ptable,
+00421 \textcolor{keywordtype}{int}   \hyperlink{fold_8h_a507d4fd93f4b398d793ba2402731388d}{loop_energy}(\textcolor{keywordtype}{short} *ptable,
 00422                   \textcolor{keywordtype}{short} *s,
 00423                   \textcolor{keywordtype}{short} *s1,
 00424                   \textcolor{keywordtype}{int} i);
@@ -154,7 +155,7 @@
 00484                                 \hyperlink{structparamT}{paramT} **P\_p);
 00485 
 00486 
-00504 \textcolor{keywordtype}{void} \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign\_plist\_from\_db}(\hyperlink{structplist}{plist} **pl,
+00504 \textcolor{keywordtype}{void} \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign_plist_from_db}(\hyperlink{structplist}{plist} **pl,
 00505                           \textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc,
 00506                           \textcolor{keywordtype}{float} pr);
 00507 
@@ -179,18 +180,18 @@
 00534                         \textcolor{keywordtype}{int} sj1,
 00535                         \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}));
 00536 
-00542 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize\_fold}(\textcolor{keywordtype}{int} length));
+00542 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize_fold}(\textcolor{keywordtype}{int} length));
 00543 
-00558 DEPRECATED(\textcolor{keywordtype}{float} \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\_of\_struct}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00558 DEPRECATED(\textcolor{keywordtype}{float} \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy_of_struct}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 00559                                   \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure));
 00560 
-00577 DEPRECATED(\textcolor{keywordtype}{int} \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\_of\_struct\_pt}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00577 DEPRECATED(\textcolor{keywordtype}{int} \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy_of_struct_pt}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 00578                                     \textcolor{keywordtype}{short} *ptable,
 00579                                     \textcolor{keywordtype}{short} *s,
 00580                                     \textcolor{keywordtype}{short} *s1));
 00581 
-00596 DEPRECATED(\textcolor{keywordtype}{float} \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\_of\_circ\_struct}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
+00596 DEPRECATED(\textcolor{keywordtype}{float} \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy_of_circ_struct}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 00597                                         \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure));
 00598 
 00599 \textcolor{preprocessor}{#endif}
-\end{DoxyCode}
+\end{alltt}\end{footnotesize}