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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / dist__vars_8h.tex

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+\hypertarget{dist__vars_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/dist\-\_\-vars.h File Reference}
+\label{dist__vars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/dist\-\_\-vars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/dist\-\_\-vars.\-h}}
+}
+
+
+Global variables for Distance-\/\-Package.  
+
+
+This graph shows which files directly or indirectly include this file\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=350pt]{dist__vars_8h__dep__incl}
+\end{center}
+\end{figure}
+\subsection*{Data Structures}
+\begin{DoxyCompactItemize}
+\item 
+struct \hyperlink{structPostorder__list}{Postorder\-\_\-list}
+\item 
+struct \hyperlink{structTree}{Tree}
+\item 
+struct \hyperlink{structswString}{sw\-String}
+\end{DoxyCompactItemize}
+\subsection*{Variables}
+\begin{DoxyCompactItemize}
+\item 
+int \hyperlink{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{edit\-\_\-backtrack}
+\begin{DoxyCompactList}\small\item\em Produce an alignment of the two structures being compared by tracing the editing path giving the minimum distance. \end{DoxyCompactList}\item 
+\hypertarget{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a}{char $\ast$ \hyperlink{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a}{aligned\-\_\-line} \mbox{[}4\mbox{]}}\label{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a}
+
+\begin{DoxyCompactList}\small\item\em Contains the two aligned structures after a call to one of the distance functions with \hyperlink{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{edit\-\_\-backtrack} set to 1. \end{DoxyCompactList}\item 
+int \hyperlink{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c}{cost\-\_\-matrix}
+\begin{DoxyCompactList}\small\item\em Specify the cost matrix to be used for distance calculations. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Global variables for Distance-\/\-Package. 
+
+\subsection{Variable Documentation}
+\hypertarget{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{\index{dist\-\_\-vars.\-h@{dist\-\_\-vars.\-h}!edit\-\_\-backtrack@{edit\-\_\-backtrack}}
+\index{edit\-\_\-backtrack@{edit\-\_\-backtrack}!dist_vars.h@{dist\-\_\-vars.\-h}}
+\subsubsection[{edit\-\_\-backtrack}]{\setlength{\rightskip}{0pt plus 5cm}int edit\-\_\-backtrack}}\label{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}
+
+
+Produce an alignment of the two structures being compared by tracing the editing path giving the minimum distance. 
+
+set to 1 if you want backtracking \hypertarget{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c}{\index{dist\-\_\-vars.\-h@{dist\-\_\-vars.\-h}!cost\-\_\-matrix@{cost\-\_\-matrix}}
+\index{cost\-\_\-matrix@{cost\-\_\-matrix}!dist_vars.h@{dist\-\_\-vars.\-h}}
+\subsubsection[{cost\-\_\-matrix}]{\setlength{\rightskip}{0pt plus 5cm}int cost\-\_\-matrix}}\label{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c}
+
+
+Specify the cost matrix to be used for distance calculations. 
+
+if 0, use the default cost matrix (upper matrix in example), otherwise use Shapiro's costs (lower matrix). 
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