\hypertarget{structTwoDfold__vars}{
\section{TwoDfold\_\-vars Struct Reference}
\label{structTwoDfold__vars}\index{TwoDfold\_\-vars@{TwoDfold\_\-vars}}
}


Variables compound for 2Dfold MFE folding.  
Collaboration diagram for TwoDfold\_\-vars:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=152pt]{structTwoDfold__vars__coll__graph}
\end{center}
\end{figure}
\subsection*{Data Fields}
\begin{DoxyCompactItemize}
\item 
\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 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}
\item 
/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/\hyperlink{data__structures_8h}{data\_\-structures.h}\end{DoxyCompactItemize}
