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

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / treedist_8h.tex

diff --git a/binaries/src/ViennaRNA/doc/latex/treedist_8h.tex b/binaries/src/ViennaRNA/doc/latex/treedist_8h.tex
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--- a/binaries/src/ViennaRNA/doc/latex/treedist_8h.tex
+++ b/binaries/src/ViennaRNA/doc/latex/treedist_8h.tex
@@ -1,91 +1,70 @@
-\hypertarget{treedist_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/treedist.h File Reference}
-\label{treedist_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/treedist.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/treedist.\-h}}
+\hypertarget{treedist_8h}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/treedist.h File Reference}
+\label{treedist_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/treedist.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/treedist.h}}
 }
 
 
 Functions for \hyperlink{structTree}{Tree} Edit Distances.  
-
-
-Include dependency graph for treedist.\-h\-:
-\nopagebreak
+Include dependency graph for treedist.h:\nopagebreak
 \begin{figure}[H]
 \begin{center}
 \leavevmode
-\includegraphics[width=250pt]{treedist_8h__incl}
+\includegraphics[width=211pt]{treedist_8h__incl}
 \end{center}
 \end{figure}
 \subsection*{Functions}
 \begin{DoxyCompactItemize}
 \item 
-\hyperlink{structTree}{Tree} $\ast$ \hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\-\_\-tree} (char $\ast$struc)
-\begin{DoxyCompactList}\small\item\em Constructs a \hyperlink{structTree}{Tree} ( essentially the postorder list ) of the structure 'struc', for use in \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\-\_\-edit\-\_\-distance()}. \end{DoxyCompactList}\item 
-float \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\-\_\-edit\-\_\-distance} (\hyperlink{structTree}{Tree} $\ast$T1, \hyperlink{structTree}{Tree} $\ast$T2)
-\begin{DoxyCompactList}\small\item\em Calculates the edit distance of the two trees. \end{DoxyCompactList}\item 
-\hypertarget{treedist_8h_a21ad4de3ba4055aeef08b28c9ad48894}{void \hyperlink{treedist_8h_a21ad4de3ba4055aeef08b28c9ad48894}{print\-\_\-tree} (\hyperlink{structTree}{Tree} $\ast$t)}\label{treedist_8h_a21ad4de3ba4055aeef08b28c9ad48894}
+\hyperlink{structTree}{Tree} $\ast$ \hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\_\-tree} (char $\ast$struc)
+\begin{DoxyCompactList}\small\item\em Constructs a \hyperlink{structTree}{Tree} ( essentially the postorder list ) of the structure 'struc', for use in \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\_\-edit\_\-distance()}. \item\end{DoxyCompactList}\item 
+float \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\_\-edit\_\-distance} (\hyperlink{structTree}{Tree} $\ast$T1, \hyperlink{structTree}{Tree} $\ast$T2)
+\begin{DoxyCompactList}\small\item\em Calculates the edit distance of the two trees. \item\end{DoxyCompactList}\item 
+\hypertarget{treedist_8h_a21ad4de3ba4055aeef08b28c9ad48894}{
+void \hyperlink{treedist_8h_a21ad4de3ba4055aeef08b28c9ad48894}{print\_\-tree} (\hyperlink{structTree}{Tree} $\ast$t)}
+\label{treedist_8h_a21ad4de3ba4055aeef08b28c9ad48894}
 
-\begin{DoxyCompactList}\small\item\em Print a tree (mainly for debugging) \end{DoxyCompactList}\item 
-void \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\-\_\-tree} (\hyperlink{structTree}{Tree} $\ast$t)
-\begin{DoxyCompactList}\small\item\em Free the memory allocated for \hyperlink{structTree}{Tree} t. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\begin{DoxyCompactList}\small\item\em Print a tree (mainly for debugging). \item\end{DoxyCompactList}\item 
+void \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\_\-tree} (\hyperlink{structTree}{Tree} $\ast$t)
+\begin{DoxyCompactList}\small\item\em Free the memory allocated for \hyperlink{structTree}{Tree} t. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
 
 
 \subsection{Detailed Description}
 Functions for \hyperlink{structTree}{Tree} Edit Distances. 
 
 \subsection{Function Documentation}
-\hypertarget{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{\index{treedist.\-h@{treedist.\-h}!make\-\_\-tree@{make\-\_\-tree}}
-\index{make\-\_\-tree@{make\-\_\-tree}!treedist.h@{treedist.\-h}}
-\subsubsection[{make\-\_\-tree}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Tree}$\ast$ make\-\_\-tree (
-\begin{DoxyParamCaption}
-\item[{char $\ast$}]{struc}
-\end{DoxyParamCaption}
-)}}\label{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}
-
-
-Constructs a \hyperlink{structTree}{Tree} ( essentially the postorder list ) of the structure 'struc', for use in \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\-\_\-edit\-\_\-distance()}. 
+\hypertarget{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{
+\index{treedist.h@{treedist.h}!make\_\-tree@{make\_\-tree}}
+\index{make\_\-tree@{make\_\-tree}!treedist.h@{treedist.h}}
+\subsubsection[{make\_\-tree}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Tree}$\ast$ make\_\-tree (char $\ast$ {\em struc})}}
+\label{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}
 
 
+Constructs a \hyperlink{structTree}{Tree} ( essentially the postorder list ) of the structure 'struc', for use in \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\_\-edit\_\-distance()}. 
 \begin{DoxyParams}{Parameters}
-{\em struc} & may be any rooted structure representation. \\
-\hline
-\end{DoxyParams}
+\item[{\em struc}]may be any rooted structure representation. \end{DoxyParams}
 \begin{DoxyReturn}{Returns}
 
 \end{DoxyReturn}
-\hypertarget{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{\index{treedist.\-h@{treedist.\-h}!tree\-\_\-edit\-\_\-distance@{tree\-\_\-edit\-\_\-distance}}
-\index{tree\-\_\-edit\-\_\-distance@{tree\-\_\-edit\-\_\-distance}!treedist.h@{treedist.\-h}}
-\subsubsection[{tree\-\_\-edit\-\_\-distance}]{\setlength{\rightskip}{0pt plus 5cm}float tree\-\_\-edit\-\_\-distance (
-\begin{DoxyParamCaption}
-\item[{{\bf Tree} $\ast$}]{T1, }
-\item[{{\bf Tree} $\ast$}]{T2}
-\end{DoxyParamCaption}
-)}}\label{treedist_8h_a3b21f1925f7071f46d93431a835217bb}
+\hypertarget{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{
+\index{treedist.h@{treedist.h}!tree\_\-edit\_\-distance@{tree\_\-edit\_\-distance}}
+\index{tree\_\-edit\_\-distance@{tree\_\-edit\_\-distance}!treedist.h@{treedist.h}}
+\subsubsection[{tree\_\-edit\_\-distance}]{\setlength{\rightskip}{0pt plus 5cm}float tree\_\-edit\_\-distance ({\bf Tree} $\ast$ {\em T1}, \/  {\bf Tree} $\ast$ {\em T2})}}
+\label{treedist_8h_a3b21f1925f7071f46d93431a835217bb}
 
 
 Calculates the edit distance of the two trees. 
-
-
 \begin{DoxyParams}{Parameters}
-{\em T1} & \\
-\hline
-{\em T2} & \\
-\hline
-\end{DoxyParams}
+\item[{\em T1}]\item[{\em T2}]\end{DoxyParams}
 \begin{DoxyReturn}{Returns}
 
 \end{DoxyReturn}
-\hypertarget{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{\index{treedist.\-h@{treedist.\-h}!free\-\_\-tree@{free\-\_\-tree}}
-\index{free\-\_\-tree@{free\-\_\-tree}!treedist.h@{treedist.\-h}}
-\subsubsection[{free\-\_\-tree}]{\setlength{\rightskip}{0pt plus 5cm}void free\-\_\-tree (
-\begin{DoxyParamCaption}
-\item[{{\bf Tree} $\ast$}]{t}
-\end{DoxyParamCaption}
-)}}\label{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}
+\hypertarget{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{
+\index{treedist.h@{treedist.h}!free\_\-tree@{free\_\-tree}}
+\index{free\_\-tree@{free\_\-tree}!treedist.h@{treedist.h}}
+\subsubsection[{free\_\-tree}]{\setlength{\rightskip}{0pt plus 5cm}void free\_\-tree ({\bf Tree} $\ast$ {\em t})}}
+\label{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}
 
 
 Free the memory allocated for \hyperlink{structTree}{Tree} t. 
-
-
 \begin{DoxyParams}{Parameters}
-{\em t} & \\
-\hline
-\end{DoxyParams}
+\item[{\em t}]\end{DoxyParams}