JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.

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

diff --git a/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars.tex b/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars.tex
index 01e0bd7..378f530 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars.tex
+++ b/binaries/src/ViennaRNA/doc/latex/structTwoDpfold__vars.tex
@@ -1,70 +1,88 @@
-\hypertarget{structTwoDpfold__vars}{\section{Two\-Dpfold\-\_\-vars Struct Reference}
-\label{structTwoDpfold__vars}\index{Two\-Dpfold\-\_\-vars@{Two\-Dpfold\-\_\-vars}}
+\hypertarget{structTwoDpfold__vars}{
+\section{TwoDpfold\_\-vars Struct Reference}
+\label{structTwoDpfold__vars}\index{TwoDpfold\_\-vars@{TwoDpfold\_\-vars}}
 }
 
 
-Variables compound for 2\-Dfold partition function folding.  
-
-
-
-
-Collaboration diagram for Two\-Dpfold\-\_\-vars\-:
-\nopagebreak
+Variables compound for 2Dfold partition function folding.  
+Collaboration diagram for TwoDpfold\_\-vars:\nopagebreak
 \begin{figure}[H]
 \begin{center}
 \leavevmode
-\includegraphics[width=184pt]{structTwoDpfold__vars__coll__graph}
+\includegraphics[width=154pt]{structTwoDpfold__vars__coll__graph}
 \end{center}
 \end{figure}
 \subsection*{Data Fields}
 \begin{DoxyCompactItemize}
 \item 
-\hypertarget{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{char $\ast$ \hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{ptype}}\label{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}
-
-\begin{DoxyCompactList}\small\item\em Precomputed array of pair types. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{char $\ast$ \hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{sequence}}\label{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}
-
-\begin{DoxyCompactList}\small\item\em The input sequence. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{short $\ast$ \hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{S1}}\label{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}
-
-\begin{DoxyCompactList}\small\item\em The input sequences in numeric form. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{unsigned int \hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{max\-D1}}\label{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}
-
-\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to first reference. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{unsigned int \hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{max\-D2}}\label{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}
-
-\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to second reference. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{int $\ast$ \hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{my\-\_\-iindx}}\label{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}
-
-\begin{DoxyCompactList}\small\item\em Index for moving in quadratic distancy dimensions. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{int $\ast$ \hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{jindx}}\label{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}
-
-\begin{DoxyCompactList}\small\item\em Index for moving in the triangular matrix qm1. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{reference\-B\-Ps1}}\label{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}
-
-\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure1 in interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{reference\-B\-Ps2}}\label{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}
-
-\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure2 in interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{bpdist}}\label{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}
-
-\begin{DoxyCompactList}\small\item\em Matrix containing base pair distance of reference structure 1 and 2 on interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{mm1}}\label{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}
-
-\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 1 disallowed. \end{DoxyCompactList}\item 
-\hypertarget{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{mm2}}\label{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}
-
-\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 2 disallowed. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\hypertarget{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{
+char $\ast$ \hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{ptype}}
+\label{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}
+
+\begin{DoxyCompactList}\small\item\em Precomputed array of pair types. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{
+char $\ast$ \hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{sequence}}
+\label{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}
+
+\begin{DoxyCompactList}\small\item\em The input sequence. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{
+short $\ast$ \hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{S1}}
+\label{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}
+
+\begin{DoxyCompactList}\small\item\em The input sequences in numeric form. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{
+unsigned int \hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{maxD1}}
+\label{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}
+
+\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to first reference. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{
+unsigned int \hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{maxD2}}
+\label{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}
+
+\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to second reference. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{
+int $\ast$ \hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{my\_\-iindx}}
+\label{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}
+
+\begin{DoxyCompactList}\small\item\em Index for moving in quadratic distancy dimensions. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{
+int $\ast$ \hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{jindx}}
+\label{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}
+
+\begin{DoxyCompactList}\small\item\em Index for moving in the triangular matrix qm1. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{
+unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{referenceBPs1}}
+\label{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}
+
+\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure1 in interval \mbox{[}i,j\mbox{]}. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{
+unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{referenceBPs2}}
+\label{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}
+
+\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure2 in interval \mbox{[}i,j\mbox{]}. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{
+unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{bpdist}}
+\label{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}
+
+\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}\item 
+\hypertarget{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{
+unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{mm1}}
+\label{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}
+
+\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 1 disallowed. \item\end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{
+unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{mm2}}
+\label{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}
+
+\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 2 disallowed. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
 
 
 \subsection{Detailed Description}
-Variables compound for 2\-Dfold partition function folding. 
-
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E()}, \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()} 
+Variables compound for 2Dfold partition function folding. \begin{DoxySeeAlso}{See also}
+\hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\_\-TwoDpfold\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\_\-TwoDpfold\_\-variables\_\-from\_\-MFE()}, \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\_\-TwoDpfold\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList()} 
 \end{DoxySeeAlso}
 
 
-The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize}
+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}
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/\hyperlink{data__structures_8h}{data\_\-structures.h}\end{DoxyCompactItemize}