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

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

diff --git a/binaries/src/ViennaRNA/doc/latex/structTwoDfold__vars.tex b/binaries/src/ViennaRNA/doc/latex/structTwoDfold__vars.tex
index 9816bc9..25f38f1 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/structTwoDfold__vars.tex
+++ b/binaries/src/ViennaRNA/doc/latex/structTwoDfold__vars.tex
@@ -1,73 +1,93 @@
-\hypertarget{structTwoDfold__vars}{\section{Two\-Dfold\-\_\-vars Struct Reference}
-\label{structTwoDfold__vars}\index{Two\-Dfold\-\_\-vars@{Two\-Dfold\-\_\-vars}}
+\hypertarget{structTwoDfold__vars}{
+\section{TwoDfold\_\-vars Struct Reference}
+\label{structTwoDfold__vars}\index{TwoDfold\_\-vars@{TwoDfold\_\-vars}}
 }
 
 
-Variables compound for 2\-Dfold M\-F\-E folding.  
-
-
-
-
-Collaboration diagram for Two\-Dfold\-\_\-vars\-:
-\nopagebreak
+Variables compound for 2Dfold MFE folding.  
+Collaboration diagram for TwoDfold\_\-vars:\nopagebreak
 \begin{figure}[H]
 \begin{center}
 \leavevmode
-\includegraphics[width=183pt]{structTwoDfold__vars__coll__graph}
+\includegraphics[width=152pt]{structTwoDfold__vars__coll__graph}
 \end{center}
 \end{figure}
 \subsection*{Data Fields}
 \begin{DoxyCompactItemize}
 \item 
-\hypertarget{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{\hyperlink{structparamT}{param\-T} $\ast$ \hyperlink{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{P}}\label{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}
-
-\begin{DoxyCompactList}\small\item\em Precomputed energy parameters and model details. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{int \hyperlink{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{do\-\_\-backtrack}}\label{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}
-
-\begin{DoxyCompactList}\small\item\em Flag whether to do backtracing of the structure(s) or not. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{char $\ast$ \hyperlink{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{ptype}}\label{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}
-
-\begin{DoxyCompactList}\small\item\em Precomputed array of pair types. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{char $\ast$ \hyperlink{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{sequence}}\label{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}
-
-\begin{DoxyCompactList}\small\item\em The input sequence. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{short $\ast$ \hyperlink{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{S1}}\label{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}
-
-\begin{DoxyCompactList}\small\item\em The input sequences in numeric form. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{unsigned int \hyperlink{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{max\-D1}}\label{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}
-
-\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to first reference. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{unsigned int \hyperlink{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{max\-D2}}\label{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}
-
-\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to second reference. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{unsigned int $\ast$ \hyperlink{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{mm1}}\label{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}
-
-\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 1 disallowed. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{unsigned int $\ast$ \hyperlink{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{mm2}}\label{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}
-
-\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 2 disallowed. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{int $\ast$ \hyperlink{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{my\-\_\-iindx}}\label{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}
-
-\begin{DoxyCompactList}\small\item\em Index for moving in quadratic distancy dimensions. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{unsigned int $\ast$ \hyperlink{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{reference\-B\-Ps1}}\label{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}
-
-\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure1 in interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{unsigned int $\ast$ \hyperlink{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{reference\-B\-Ps2}}\label{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}
-
-\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure2 in interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{unsigned int $\ast$ \hyperlink{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{bpdist}}\label{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}
-
-\begin{DoxyCompactList}\small\item\em Matrix containing base pair distance of reference structure 1 and 2 on interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\hypertarget{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{
+\hyperlink{structparamT}{paramT} $\ast$ \hyperlink{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}{P}}
+\label{structTwoDfold__vars_ada74adef5f24b4b35c0b25da8223fe26}
+
+\begin{DoxyCompactList}\small\item\em Precomputed energy parameters and model details. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{
+int \hyperlink{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}{do\_\-backtrack}}
+\label{structTwoDfold__vars_ade5c7e9337a458ae20bac75abdc52d64}
+
+\begin{DoxyCompactList}\small\item\em Flag whether to do backtracing of the structure(s) or not. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{
+char $\ast$ \hyperlink{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}{ptype}}
+\label{structTwoDfold__vars_aedf60b8b26dae05ad266d3e098d18208}
+
+\begin{DoxyCompactList}\small\item\em Precomputed array of pair types. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{
+char $\ast$ \hyperlink{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}{sequence}}
+\label{structTwoDfold__vars_a3596f3d4d320318c4b8428e2abc7ab56}
+
+\begin{DoxyCompactList}\small\item\em The input sequence. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{
+short $\ast$ \hyperlink{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}{S1}}
+\label{structTwoDfold__vars_ab9ee459ffbfb5d2c138a033516056cdc}
+
+\begin{DoxyCompactList}\small\item\em The input sequences in numeric form. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{
+unsigned int \hyperlink{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}{maxD1}}
+\label{structTwoDfold__vars_a621ed2ab02116f3f8f5e7120dec429eb}
+
+\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to first reference. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{
+unsigned int \hyperlink{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}{maxD2}}
+\label{structTwoDfold__vars_a03f198a4abdb3b784486d2ba5c533aa4}
+
+\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to second reference. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{
+unsigned int $\ast$ \hyperlink{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}{mm1}}
+\label{structTwoDfold__vars_aa11f5bcd8c4fe70a91c155c877c855d5}
+
+\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 1 disallowed. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{
+unsigned int $\ast$ \hyperlink{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}{mm2}}
+\label{structTwoDfold__vars_a2eaa93316b6beb17531f0c078806036c}
+
+\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 2 disallowed. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{
+int $\ast$ \hyperlink{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}{my\_\-iindx}}
+\label{structTwoDfold__vars_a1a20cb06b58b75d1a3dbdbc8bc60d0a7}
+
+\begin{DoxyCompactList}\small\item\em Index for moving in quadratic distancy dimensions. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{
+unsigned int $\ast$ \hyperlink{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}{referenceBPs1}}
+\label{structTwoDfold__vars_a536525b98c1b633d4c5f2da4f8d78c18}
+
+\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure1 in interval \mbox{[}i,j\mbox{]}. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{
+unsigned int $\ast$ \hyperlink{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}{referenceBPs2}}
+\label{structTwoDfold__vars_aa7abf73c3114cb5f0dc90e702fa9dd0f}
+
+\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure2 in interval \mbox{[}i,j\mbox{]}. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{
+unsigned int $\ast$ \hyperlink{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}{bpdist}}
+\label{structTwoDfold__vars_af1106e1a592e2dccc92b3452340549e0}
+
+\begin{DoxyCompactList}\small\item\em Matrix containing base pair distance of reference structure 1 and 2 on interval \mbox{[}i,j\mbox{]}. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
 
 
 \subsection{Detailed Description}
-Variables compound for 2\-Dfold M\-F\-E folding. 
-
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{get\-\_\-\-Two\-Dfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__mfe_ga05bf4f31d216b1b160fd2d3d68e9b487}{destroy\-\_\-\-Two\-Dfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{Two\-Dfold\-List()} 
+Variables compound for 2Dfold MFE folding. \begin{DoxySeeAlso}{See also}
+\hyperlink{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{get\_\-TwoDfold\_\-variables()}, \hyperlink{group__kl__neighborhood__mfe_ga05bf4f31d216b1b160fd2d3d68e9b487}{destroy\_\-TwoDfold\_\-variables()}, \hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{TwoDfoldList()} 
 \end{DoxySeeAlso}
 
 
-The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize}
+The documentation for this struct was generated from the following file:\begin{DoxyCompactItemize}
 \item 
-/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize}
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/\hyperlink{data__structures_8h}{data\_\-structures.h}\end{DoxyCompactItemize}