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

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+\hypertarget{structTwoDfold__vars}{\section{Two\-Dfold\-\_\-vars Struct Reference}
+\label{structTwoDfold__vars}\index{Two\-Dfold\-\_\-vars@{Two\-Dfold\-\_\-vars}}
+}
+
+
+Variables compound for 2\-Dfold M\-F\-E folding.  
+
+
+
+
+Collaboration diagram for Two\-Dfold\-\_\-vars\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=183pt]{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}
+
+
+\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()} 
+\end{DoxySeeAlso}
+
+
+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}