\hypertarget{dist__vars_8h}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/dist\_\-vars.h File Reference}
\label{dist__vars_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/dist\_\-vars.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/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=413pt]{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}{swString}
\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. \item\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. \item\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. \item\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 {\bf 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 {\bf 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). 