binaries/src/ViennaRNA/doc/latex/dist__vars_8h.tex

   1 \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}
   2 \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}}
   3 }
   4
   5
   6 Global variables for Distance-\/\-Package.
   7
   8
   9 This graph shows which files directly or indirectly include this file\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=350pt]{dist__vars_8h__dep__incl}
  15 \end{center}
  16 \end{figure}
  17 \subsection*{Data Structures}
  18 \begin{DoxyCompactItemize}
  19 \item
  20 struct \hyperlink{structPostorder__list}{Postorder\-\_\-list}
  21 \item
  22 struct \hyperlink{structTree}{Tree}
  23 \item
  24 struct \hyperlink{structswString}{sw\-String}
  25 \end{DoxyCompactItemize}
  26 \subsection*{Variables}
  27 \begin{DoxyCompactItemize}
  28 \item
  29 int \hyperlink{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{edit\-\_\-backtrack}
  30 \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
  31 \hypertarget{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a}{char $\ast$ \hyperlink{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a}{aligned\-\_\-line} \mbox{[}4\mbox{]}}\label{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a}
  32
  33 \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
  34 int \hyperlink{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c}{cost\-\_\-matrix}
  35 \begin{DoxyCompactList}\small\item\em Specify the cost matrix to be used for distance calculations. \end{DoxyCompactList}\end{DoxyCompactItemize}
  36
  37
  38 \subsection{Detailed Description}
  39 Global variables for Distance-\/\-Package.
  40
  41 \subsection{Variable Documentation}
  42 \hypertarget{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{\index{dist\-\_\-vars.\-h@{dist\-\_\-vars.\-h}!edit\-\_\-backtrack@{edit\-\_\-backtrack}}
  43 \index{edit\-\_\-backtrack@{edit\-\_\-backtrack}!dist_vars.h@{dist\-\_\-vars.\-h}}
  44 \subsubsection[{edit\-\_\-backtrack}]{\setlength{\rightskip}{0pt plus 5cm}int edit\-\_\-backtrack}}\label{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}
  45
  46
  47 Produce an alignment of the two structures being compared by tracing the editing path giving the minimum distance.
  48
  49 set to 1 if you want backtracking \hypertarget{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c}{\index{dist\-\_\-vars.\-h@{dist\-\_\-vars.\-h}!cost\-\_\-matrix@{cost\-\_\-matrix}}
  50 \index{cost\-\_\-matrix@{cost\-\_\-matrix}!dist_vars.h@{dist\-\_\-vars.\-h}}
  51 \subsubsection[{cost\-\_\-matrix}]{\setlength{\rightskip}{0pt plus 5cm}int cost\-\_\-matrix}}\label{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c}
  52
  53
  54 Specify the cost matrix to be used for distance calculations.
  55
  56 if 0, use the default cost matrix (upper matrix in example), otherwise use Shapiro's costs (lower matrix).