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

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / 2Dpfold_8h.tex

diff --git a/binaries/src/ViennaRNA/doc/latex/2Dpfold_8h.tex b/binaries/src/ViennaRNA/doc/latex/2Dpfold_8h.tex
index af9d609..122fa3c 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/2Dpfold_8h.tex
+++ b/binaries/src/ViennaRNA/doc/latex/2Dpfold_8h.tex
@@ -1,26 +1,29 @@
-\hypertarget{2Dpfold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.h File Reference}
-\label{2Dpfold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.\-h}}
+\hypertarget{2Dpfold_8h}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h File Reference}
+\label{2Dpfold_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h}}
 }
-Include dependency graph for 2\-Dpfold.h\-:
-\nopagebreak
+Include dependency graph for 2Dpfold.h:\nopagebreak
 \begin{figure}[H]
 \begin{center}
 \leavevmode
-\includegraphics[width=250pt]{2Dpfold_8h__incl}
+\includegraphics[width=212pt]{2Dpfold_8h__incl}
 \end{center}
 \end{figure}
 \subsection*{Functions}
 \begin{DoxyCompactItemize}
 \item 
-\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables} (const char $\ast$seq, const char $\ast$structure1, char $\ast$structure2, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ})
-\begin{DoxyCompactList}\small\item\em Get a datastructure containing all necessary attributes and global folding switches. \end{DoxyCompactList}\item 
-\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E} (\hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$mfe\-\_\-vars)
-\begin{DoxyCompactList}\small\item\em Get the datastructure containing all necessary attributes and global folding switches from a pre-\/filled mfe-\/datastructure. \end{DoxyCompactList}\item 
-void \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\-\_\-\-Two\-Dpfold\-\_\-variables} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars)
-\begin{DoxyCompactList}\small\item\em Free all memory occupied by a \hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} datastructure. \end{DoxyCompactList}\item 
-\hyperlink{structTwoDpfold__solution}{Two\-Dpfold\-\_\-solution} $\ast$ \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars, int max\-Distance1, int max\-Distance2)
-\begin{DoxyCompactList}\small\item\em Compute the partition function for all distance classes. \end{DoxyCompactList}\item 
-char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{Two\-Dpfold\-\_\-pbacktrack} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars, int d1, int d2)
-\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. \end{DoxyCompactList}\item 
-char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{Two\-Dpfold\-\_\-pbacktrack5} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars, int d1, int d2, unsigned int length)
-\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\_\-TwoDpfold\_\-variables} (const char $\ast$seq, const char $\ast$structure1, char $\ast$structure2, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ})
+\begin{DoxyCompactList}\small\item\em Get a datastructure containing all necessary attributes and global folding switches. \item\end{DoxyCompactList}\item 
+\hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\_\-TwoDpfold\_\-variables\_\-from\_\-MFE} (\hyperlink{structTwoDfold__vars}{TwoDfold\_\-vars} $\ast$mfe\_\-vars)
+\begin{DoxyCompactList}\small\item\em Get the datastructure containing all necessary attributes and global folding switches from a pre-\/filled mfe-\/datastructure. \item\end{DoxyCompactList}\item 
+void \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\_\-TwoDpfold\_\-variables} (\hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} $\ast$vars)
+\begin{DoxyCompactList}\small\item\em Free all memory occupied by a \hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} datastructure. \item\end{DoxyCompactList}\item 
+\hyperlink{structTwoDpfold__solution}{TwoDpfold\_\-solution} $\ast$ \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList} (\hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} $\ast$vars, int maxDistance1, int maxDistance2)
+\begin{DoxyCompactList}\small\item\em Compute the partition function for all distance classes. \item\end{DoxyCompactList}\item 
+char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{TwoDpfold\_\-pbacktrack} (\hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} $\ast$vars, int d1, int d2)
+\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. \item\end{DoxyCompactList}\item 
+char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{TwoDpfold\_\-pbacktrack5} (\hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} $\ast$vars, int d1, int d2, unsigned int length)
+\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}