JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / alifold_8h_source.tex

diff --git a/binaries/src/ViennaRNA/doc/latex/alifold_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/alifold_8h_source.tex
index 3191f07..63c2962 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/alifold_8h_source.tex
+++ b/binaries/src/ViennaRNA/doc/latex/alifold_8h_source.tex
@@ -1,15 +1,16 @@
-\hypertarget{alifold_8h}{\section{alifold.\-h}
-\label{alifold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/alifold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/alifold.\-h}}
+\hypertarget{alifold_8h_source}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h}
 }
 
-\begin{DoxyCode}
+
+\begin{footnotesize}\begin{alltt}
 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_ALIFOLD\_H\_\_}
 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_ALIFOLD\_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 
-00043 \textcolor{keyword}{extern}  \textcolor{keywordtype}{double}  \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv\_fact};
-00052 \textcolor{keyword}{extern}  \textcolor{keywordtype}{double}  \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc\_fact};
+00043 \textcolor{keyword}{extern}  \textcolor{keywordtype}{double}  \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv_fact};
+00052 \textcolor{keyword}{extern}  \textcolor{keywordtype}{double}  \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc_fact};
 00053 
 00054 \textcolor{comment}{/*}
 00055 \textcolor{comment}{##############################################}
@@ -17,7 +18,7 @@
 00057 \textcolor{comment}{##############################################}
 00058 \textcolor{comment}{*/}
 00059 
-00066 \textcolor{keywordtype}{void} \hyperlink{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{update\_alifold\_params}(\textcolor{keywordtype}{void});
+00066 \textcolor{keywordtype}{void} \hyperlink{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{update_alifold_params}(\textcolor{keywordtype}{void});
 00067 
 00068 
 00086 \textcolor{keywordtype}{float}  \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings,
@@ -27,16 +28,16 @@
 00100 \textcolor{keywordtype}{float}  \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **strings,
 00101                     \textcolor{keywordtype}{char} *structure);
 00102 
-00109 \textcolor{keywordtype}{void}    \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free\_alifold\_arrays}(\textcolor{keywordtype}{void});
+00109 \textcolor{keywordtype}{void}    \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free_alifold_arrays}(\textcolor{keywordtype}{void});
 00110 
-00122 \textcolor{keywordtype}{int} \hyperlink{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{get\_mpi}(\textcolor{keywordtype}{char} *Alseq[],
+00122 \textcolor{keywordtype}{int} \hyperlink{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{get_mpi}(\textcolor{keywordtype}{char} *Alseq[],
 00123             \textcolor{keywordtype}{int} n\_seq,
 00124             \textcolor{keywordtype}{int} length,
 00125             \textcolor{keywordtype}{int} *mini);
 00126 
 00133 \textcolor{keywordtype}{float}   **\hyperlink{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{readribosum}(\textcolor{keywordtype}{char} *name);
 00134 
-00148 \textcolor{keywordtype}{float}   \hyperlink{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{energy\_of\_alistruct}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
+00148 \textcolor{keywordtype}{float}   \hyperlink{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{energy_of_alistruct}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
 00149                             \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure,
 00150                             \textcolor{keywordtype}{int} n\_seq,
 00151                             \textcolor{keywordtype}{float} *energy);
@@ -52,7 +53,7 @@
 00161 \textcolor{comment}{#############################################################}
 00162 \textcolor{comment}{*/}
 00163 
-00180 \textcolor{keywordtype}{void} \hyperlink{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{encode\_ali\_sequence}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
+00180 \textcolor{keywordtype}{void} \hyperlink{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{encode_ali_sequence}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
 00181                           \textcolor{keywordtype}{short} *S,
 00182                           \textcolor{keywordtype}{short} *s5,
 00183                           \textcolor{keywordtype}{short} *s3,
@@ -60,7 +61,7 @@
 00185                           \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} *as,
 00186                           \textcolor{keywordtype}{int} circ);
 00187 
-00205 \textcolor{keywordtype}{void}  \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\_sequence\_arrays}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
+00205 \textcolor{keywordtype}{void}  \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc_sequence_arrays}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
 00206                             \textcolor{keywordtype}{short} ***S,
 00207                             \textcolor{keywordtype}{short} ***S5,
 00208                             \textcolor{keywordtype}{short} ***S3,
@@ -68,7 +69,7 @@
 00210                             \textcolor{keywordtype}{char} ***Ss,
 00211                             \textcolor{keywordtype}{int} circ);
 00212 
-00229 \textcolor{keywordtype}{void}  \hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free\_sequence\_arrays}( \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} n\_seq,
+00229 \textcolor{keywordtype}{void}  \hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free_sequence_arrays}( \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} n\_seq,
 00230                             \textcolor{keywordtype}{short} ***S,
 00231                             \textcolor{keywordtype}{short} ***S5,
 00232                             \textcolor{keywordtype}{short} ***S3,
@@ -82,31 +83,31 @@
 00240 \textcolor{comment}{*/}
 00241 
 00242 
-00265 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf\_fold\_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
+00265 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf_fold_par}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
 00266                       \textcolor{keywordtype}{char} *structure,
 00267                       \hyperlink{structplist}{plist} **pl,
-00268                       \hyperlink{structpf__paramT}{pf\_paramT} *parameters,
+00268                       \hyperlink{structpf__paramT}{pf_paramT} *parameters,
 00269                       \textcolor{keywordtype}{int} calculate\_bppm,
 00270                       \textcolor{keywordtype}{int} is\_constrained,
 00271                       \textcolor{keywordtype}{int} is\_circular);
 00272 
-00289 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\_fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
+00289 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf_fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
 00290                   \textcolor{keywordtype}{char} *structure,
 00291                   \hyperlink{structplist}{plist} **pl);
 00292 
-00303 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\_circ\_fold}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
+00303 \textcolor{keywordtype}{float} \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf_circ_fold}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,
 00304                       \textcolor{keywordtype}{char} *structure,
 00305                       \hyperlink{structplist}{plist} **pl);
 00306 
 00307 
-00319 FLT\_OR\_DBL *\hyperlink{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{export\_ali\_bppm}(\textcolor{keywordtype}{void});
+00319 FLT\_OR\_DBL *\hyperlink{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}{export_ali_bppm}(\textcolor{keywordtype}{void});
 00320 
 00327 \textcolor{keywordtype}{void}  free\_alipf\_arrays(\textcolor{keywordtype}{void});
 00328 
 00344 \textcolor{keywordtype}{char}  *\hyperlink{group__consensus__stochbt_ga0df40248788f0fb17ebdc59d74116d1c}{alipbacktrack}(\textcolor{keywordtype}{double} *prob);
 00345 
 00346 
-00367 \textcolor{keywordtype}{int} \hyperlink{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}{get\_alipf\_arrays}(\textcolor{keywordtype}{short} ***S\_p,
+00367 \textcolor{keywordtype}{int} \hyperlink{group__consensus__fold_ga5349960075b1847720a2e9df021e2675}{get_alipf_arrays}(\textcolor{keywordtype}{short} ***S\_p,
 00368          \textcolor{keywordtype}{short} ***S5\_p,
 00369          \textcolor{keywordtype}{short} ***S3\_p,
 00370          \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} ***a2s\_p,
@@ -118,4 +119,4 @@
 00376          \textcolor{keywordtype}{short} **pscore);
 00377 
 00378 \textcolor{preprocessor}{#endif}
-\end{DoxyCode}
+\end{alltt}\end{footnotesize}