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

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / convert__epars_8h.tex

diff --git a/binaries/src/ViennaRNA/doc/latex/convert__epars_8h.tex b/binaries/src/ViennaRNA/doc/latex/convert__epars_8h.tex
index 61430bf..e95f2d0 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/convert__epars_8h.tex
+++ b/binaries/src/ViennaRNA/doc/latex/convert__epars_8h.tex
@@ -1,62 +1,61 @@
-\hypertarget{convert__epars_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/convert\-\_\-epars.h File Reference}
-\label{convert__epars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/convert\-\_\-epars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/convert\-\_\-epars.\-h}}
+\hypertarget{convert__epars_8h}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/convert\_\-epars.h File Reference}
+\label{convert__epars_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/convert\_\-epars.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/convert\_\-epars.h}}
 }
 
 
 Functions and definitions for energy parameter file format conversion.  
-
-
-\subsection*{Macros}
+\subsection*{Defines}
 \begin{DoxyCompactItemize}
 \item 
-\#define \hyperlink{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-A\-L\-L}~1\-U
+\#define \hyperlink{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{VRNA\_\-CONVERT\_\-OUTPUT\_\-ALL}~1U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-H\-P}~2\-U
+\#define \hyperlink{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{VRNA\_\-CONVERT\_\-OUTPUT\_\-HP}~2U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-T\-A\-C\-K}~4\-U
+\#define \hyperlink{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{VRNA\_\-CONVERT\_\-OUTPUT\_\-STACK}~4U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-H\-P}~8\-U
+\#define \hyperlink{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-HP}~8U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T}~16\-U
+\#define \hyperlink{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT}~16U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-1\-N}~32\-U
+\#define \hyperlink{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-1N}~32U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-23}~64\-U
+\#define \hyperlink{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-23}~64U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-M\-U\-L\-T\-I}~128\-U
+\#define \hyperlink{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-MULTI}~128U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-E\-X\-T}~256\-U
+\#define \hyperlink{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-EXT}~256U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E5}~512\-U
+\#define \hyperlink{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE5}~512U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E3}~1024\-U
+\#define \hyperlink{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE3}~1024U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-11}~2048\-U
+\#define \hyperlink{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-11}~2048U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-21}~4096\-U
+\#define \hyperlink{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-21}~4096U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-22}~8192\-U
+\#define \hyperlink{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-22}~8192U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-B\-U\-L\-G\-E}~16384\-U
+\#define \hyperlink{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{VRNA\_\-CONVERT\_\-OUTPUT\_\-BULGE}~16384U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T}~32768\-U
+\#define \hyperlink{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT}~32768U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-L}~65536\-U
+\#define \hyperlink{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{VRNA\_\-CONVERT\_\-OUTPUT\_\-ML}~65536U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-I\-S\-C}~131072\-U
+\#define \hyperlink{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MISC}~131072U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-P\-E\-C\-I\-A\-L\-\_\-\-H\-P}~262144\-U
+\#define \hyperlink{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{VRNA\_\-CONVERT\_\-OUTPUT\_\-SPECIAL\_\-HP}~262144U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-V\-A\-N\-I\-L\-L\-A}~524288\-U
+\#define \hyperlink{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{VRNA\_\-CONVERT\_\-OUTPUT\_\-VANILLA}~524288U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-N\-I\-N\-I\-O}~1048576\-U
+\#define \hyperlink{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{VRNA\_\-CONVERT\_\-OUTPUT\_\-NINIO}~1048576U
 \item 
-\#define \hyperlink{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P}~2097152\-U
+\#define \hyperlink{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DUMP}~2097152U
 \end{DoxyCompactItemize}
 \subsection*{Functions}
 \begin{DoxyCompactItemize}
 \item 
-void \hyperlink{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}{convert\-\_\-parameter\-\_\-file} (const char $\ast$iname, const char $\ast$oname, unsigned int options)
+void \hyperlink{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}{convert\_\-parameter\_\-file} (const char $\ast$iname, const char $\ast$oname, unsigned int options)
 \end{DoxyCompactItemize}