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

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / params_8h.tex

diff --git a/binaries/src/ViennaRNA/doc/latex/params_8h.tex b/binaries/src/ViennaRNA/doc/latex/params_8h.tex
index cb38616..e9d7819 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/params_8h.tex
+++ b/binaries/src/ViennaRNA/doc/latex/params_8h.tex
@@ -1,38 +1,44 @@
-\hypertarget{params_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/params.h File Reference}
-\label{params_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/params.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/params.\-h}}
+\hypertarget{params_8h}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/params.h File Reference}
+\label{params_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/params.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/params.h}}
 }
-Include dependency graph for params.\-h\-:
-\nopagebreak
+Include dependency graph for params.h:\nopagebreak
 \begin{figure}[H]
 \begin{center}
 \leavevmode
-\includegraphics[width=250pt]{params_8h__incl}
+\includegraphics[width=212pt]{params_8h__incl}
 \end{center}
 \end{figure}
-This graph shows which files directly or indirectly include this file\-:
-\nopagebreak
+This graph shows which files directly or indirectly include this file:\nopagebreak
 \begin{figure}[H]
 \begin{center}
 \leavevmode
-\includegraphics[width=250pt]{params_8h__dep__incl}
+\includegraphics[width=227pt]{params_8h__dep__incl}
 \end{center}
 \end{figure}
 \subsection*{Functions}
 \begin{DoxyCompactItemize}
 \item 
-\hyperlink{structparamT}{param\-T} $\ast$ \hyperlink{group__energy__parameters_ga527ef619cd8210b84d5d53be1e0e29b6}{scale\-\_\-parameters} (void)
-\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \end{DoxyCompactList}\item 
-\hyperlink{structparamT}{param\-T} $\ast$ \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} md)
-\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \end{DoxyCompactList}\item 
-\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\-\_\-scaled\-\_\-pf\-\_\-parameters} (void)
+\hyperlink{structparamT}{paramT} $\ast$ \hyperlink{group__energy__parameters_ga527ef619cd8210b84d5d53be1e0e29b6}{scale\_\-parameters} (void)
+\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \item\end{DoxyCompactList}\item 
+\hyperlink{structparamT}{paramT} $\ast$ \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\_\-scaled\_\-parameters} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, \hyperlink{structmodel__detailsT}{model\_\-detailsT} md)
+\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \item\end{DoxyCompactList}\item 
+\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$ \hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\_\-scaled\_\-pf\_\-parameters} (void)
 \item 
-\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{get\-\_\-boltzmann\-\_\-factors} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double beta\-Scale, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} md, double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale})
-\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature. \end{DoxyCompactList}\item 
-\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gacba212326a051734797e65987260fdd0}{get\-\_\-boltzmann\-\_\-factor\-\_\-copy} (\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters)
-\begin{DoxyCompactList}\small\item\em Get a copy of already precomputed Boltzmann factors. \end{DoxyCompactList}\item 
-\hypertarget{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{get\-\_\-scaled\-\_\-alipf\-\_\-parameters} (unsigned int n\-\_\-seq)}\label{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}
+\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$ \hyperlink{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{get\_\-boltzmann\_\-factors} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double betaScale, \hyperlink{structmodel__detailsT}{model\_\-detailsT} md, double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\_\-scale})
+\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature. \item\end{DoxyCompactList}\item 
+\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$ \hyperlink{group__energy__parameters_gacba212326a051734797e65987260fdd0}{get\_\-boltzmann\_\-factor\_\-copy} (\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$parameters)
+\begin{DoxyCompactList}\small\item\em Get a copy of already precomputed Boltzmann factors. \item\end{DoxyCompactList}\item 
+\hypertarget{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{
+\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$ \hyperlink{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{get\_\-scaled\_\-alipf\_\-parameters} (unsigned int n\_\-seq)}
+\label{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}
 
-\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) \end{DoxyCompactList}\item 
-\hypertarget{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66}{P\-U\-B\-L\-I\-C \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66}{get\-\_\-boltzmann\-\_\-factors\-\_\-ali} (unsigned int n\-\_\-seq, double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double beta\-Scale, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} md, double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale})}\label{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66}
+\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant). \item\end{DoxyCompactList}\item 
+\hypertarget{group__energy__parameters_gaf0c74574b40f2778556535bf9d382828}{
+\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$ \hyperlink{group__energy__parameters_gaf0c74574b40f2778556535bf9d382828}{get\_\-boltzmann\_\-factors\_\-ali} (unsigned int n\_\-seq, double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double betaScale, \hyperlink{structmodel__detailsT}{model\_\-detailsT} md, double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\_\-scale})}
+\label{group__energy__parameters_gaf0c74574b40f2778556535bf9d382828}
 
-\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) with independent thermodynamic temperature. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) with independent thermodynamic temperature. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}