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

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / LPfold_8h.tex

diff --git a/binaries/src/ViennaRNA/doc/latex/LPfold_8h.tex b/binaries/src/ViennaRNA/doc/latex/LPfold_8h.tex
index 740a045..2df12dc 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/LPfold_8h.tex
+++ b/binaries/src/ViennaRNA/doc/latex/LPfold_8h.tex
@@ -1,34 +1,34 @@
-\hypertarget{LPfold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-L\-Pfold.h File Reference}
-\label{LPfold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-L\-Pfold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-L\-Pfold.\-h}}
+\hypertarget{LPfold_8h}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/LPfold.h File Reference}
+\label{LPfold_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/LPfold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/LPfold.h}}
 }
 
 
 Function declarations of partition function variants of the Lfold algorithm.  
-
-
-Include dependency graph for L\-Pfold.\-h\-:
-\nopagebreak
+Include dependency graph for LPfold.h:\nopagebreak
 \begin{figure}[H]
 \begin{center}
 \leavevmode
-\includegraphics[width=250pt]{LPfold_8h__incl}
+\includegraphics[width=209pt]{LPfold_8h__incl}
 \end{center}
 \end{figure}
 \subsection*{Functions}
 \begin{DoxyCompactItemize}
 \item 
-void \hyperlink{group__local__pf__fold_ga5a019014d37fe6105131dfc2fc447880}{update\-\_\-pf\-\_\-params\-L\-P} (int length)
+void \hyperlink{group__local__pf__fold_ga5a019014d37fe6105131dfc2fc447880}{update\_\-pf\_\-paramsLP} (int length)
 \item 
-\hyperlink{structplist}{plist} $\ast$ \hyperlink{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}{pfl\-\_\-fold} (char $\ast$sequence, int win\-Size, int pair\-Size, float cutoffb, double $\ast$$\ast$p\-U, struct \hyperlink{structplist}{plist} $\ast$$\ast$dpp2, F\-I\-L\-E $\ast$p\-Ufp, F\-I\-L\-E $\ast$spup)
-\begin{DoxyCompactList}\small\item\em Compute partition functions for locally stable secondary structures. \end{DoxyCompactList}\item 
-\hypertarget{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}{\hyperlink{structplist}{plist} $\ast$ \hyperlink{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}{pfl\-\_\-fold\-\_\-par} (char $\ast$sequence, int win\-Size, int pair\-Size, float cutoffb, double $\ast$$\ast$p\-U, struct \hyperlink{structplist}{plist} $\ast$$\ast$dpp2, F\-I\-L\-E $\ast$p\-Ufp, F\-I\-L\-E $\ast$spup, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters)}\label{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}
-
-\begin{DoxyCompactList}\small\item\em Compute partition functions for locally stable secondary structures. \end{DoxyCompactList}\item 
-void \hyperlink{group__local__pf__fold_ga0bcb751860bbf34e3dfee8c2fbdb3ef3}{putoutp\-U\-\_\-prob} (double $\ast$$\ast$p\-U, int length, int ulength, F\-I\-L\-E $\ast$fp, int energies)
-\begin{DoxyCompactList}\small\item\em Writes the unpaired probabilities (p\-U) or opening energies into a file. \end{DoxyCompactList}\item 
-void \hyperlink{group__local__pf__fold_ga9acb00ee10e96b1ca4ea394cd8bcec75}{putoutp\-U\-\_\-prob\-\_\-bin} (double $\ast$$\ast$p\-U, int length, int ulength, F\-I\-L\-E $\ast$fp, int energies)
-\begin{DoxyCompactList}\small\item\em Writes the unpaired probabilities (p\-U) or opening energies into a binary file. \end{DoxyCompactList}\item 
-void \hyperlink{LPfold_8h_ae85bf55053e9fb295208be322e0fa07a}{init\-\_\-pf\-\_\-fold\-L\-P} (int length)
+\hyperlink{structplist}{plist} $\ast$ \hyperlink{group__local__pf__fold_gaa1ecd401617ebc748a0220026543c777}{pfl\_\-fold} (char $\ast$sequence, int winSize, int pairSize, float cutoffb, double $\ast$$\ast$pU, struct \hyperlink{structplist}{plist} $\ast$$\ast$dpp2, FILE $\ast$pUfp, FILE $\ast$spup)
+\begin{DoxyCompactList}\small\item\em Compute partition functions for locally stable secondary structures. \item\end{DoxyCompactList}\item 
+\hypertarget{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}{
+\hyperlink{structplist}{plist} $\ast$ \hyperlink{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}{pfl\_\-fold\_\-par} (char $\ast$sequence, int winSize, int pairSize, float cutoffb, double $\ast$$\ast$pU, struct \hyperlink{structplist}{plist} $\ast$$\ast$dpp2, FILE $\ast$pUfp, FILE $\ast$spup, \hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$parameters)}
+\label{group__local__pf__fold_gab354507e8028f3e1c52ef96bb1eb9df8}
+
+\begin{DoxyCompactList}\small\item\em Compute partition functions for locally stable secondary structures. \item\end{DoxyCompactList}\item 
+void \hyperlink{group__local__pf__fold_ga0bcb751860bbf34e3dfee8c2fbdb3ef3}{putoutpU\_\-prob} (double $\ast$$\ast$pU, int length, int ulength, FILE $\ast$fp, int energies)
+\begin{DoxyCompactList}\small\item\em Writes the unpaired probabilities (pU) or opening energies into a file. \item\end{DoxyCompactList}\item 
+void \hyperlink{group__local__pf__fold_ga9acb00ee10e96b1ca4ea394cd8bcec75}{putoutpU\_\-prob\_\-bin} (double $\ast$$\ast$pU, int length, int ulength, FILE $\ast$fp, int energies)
+\begin{DoxyCompactList}\small\item\em Writes the unpaired probabilities (pU) or opening energies into a binary file. \item\end{DoxyCompactList}\item 
+void \hyperlink{LPfold_8h_ae85bf55053e9fb295208be322e0fa07a}{init\_\-pf\_\-foldLP} (int length)
 \end{DoxyCompactItemize}
 
 
@@ -36,11 +36,9 @@ void \hyperlink{LPfold_8h_ae85bf55053e9fb295208be322e0fa07a}{init\-\_\-pf\-\_\-f
 Function declarations of partition function variants of the Lfold algorithm. 
 
 \subsection{Function Documentation}
-\hypertarget{LPfold_8h_ae85bf55053e9fb295208be322e0fa07a}{\index{L\-Pfold.\-h@{L\-Pfold.\-h}!init\-\_\-pf\-\_\-fold\-L\-P@{init\-\_\-pf\-\_\-fold\-L\-P}}
-\index{init\-\_\-pf\-\_\-fold\-L\-P@{init\-\_\-pf\-\_\-fold\-L\-P}!LPfold.h@{L\-Pfold.\-h}}
-\subsubsection[{init\-\_\-pf\-\_\-fold\-L\-P}]{\setlength{\rightskip}{0pt plus 5cm}void init\-\_\-pf\-\_\-fold\-L\-P (
-\begin{DoxyParamCaption}
-\item[{int}]{length}
-\end{DoxyParamCaption}
-)}}\label{LPfold_8h_ae85bf55053e9fb295208be322e0fa07a}
-Dunno if this function was ever used by external programs linking to R\-N\-Alib, but it was declared P\-U\-B\-L\-I\-C before. Anyway, never use this function as it will be removed soon and does nothing at all 
\ No newline at end of file
+\hypertarget{LPfold_8h_ae85bf55053e9fb295208be322e0fa07a}{
+\index{LPfold.h@{LPfold.h}!init\_\-pf\_\-foldLP@{init\_\-pf\_\-foldLP}}
+\index{init\_\-pf\_\-foldLP@{init\_\-pf\_\-foldLP}!LPfold.h@{LPfold.h}}
+\subsubsection[{init\_\-pf\_\-foldLP}]{\setlength{\rightskip}{0pt plus 5cm}void init\_\-pf\_\-foldLP (int {\em length})}}
+\label{LPfold_8h_ae85bf55053e9fb295208be322e0fa07a}
+Dunno if this function was ever used by external programs linking to RNAlib, but it was declared PUBLIC before. Anyway, never use this function as it will be removed soon and does nothing at all 
\ No newline at end of file