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

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / pair__mat_8h_source.tex

diff --git a/binaries/src/ViennaRNA/doc/latex/pair__mat_8h_source.tex b/binaries/src/ViennaRNA/doc/latex/pair__mat_8h_source.tex
index c970d82..fe79732 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/pair__mat_8h_source.tex
+++ b/binaries/src/ViennaRNA/doc/latex/pair__mat_8h_source.tex
@@ -1,11 +1,12 @@
-\hypertarget{pair__mat_8h}{\section{pair\-\_\-mat.\-h}
-\label{pair__mat_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/pair\-\_\-mat.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/pair\-\_\-mat.\-h}}
+\hypertarget{pair__mat_8h_source}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/pair\_\-mat.h}
 }
 
-\begin{DoxyCode}
+
+\begin{footnotesize}\begin{alltt}
 00001 \textcolor{preprocessor}{#include <ctype.h>}
 00002 \textcolor{preprocessor}{#include "\hyperlink{utils_8h}{utils.h}"}
-00003 \textcolor{preprocessor}{#include "\hyperlink{fold__vars_8h}{fold\_vars.h}"}
+00003 \textcolor{preprocessor}{#include "\hyperlink{fold__vars_8h}{fold_vars.h}"}
 00004 
 00005 \textcolor{preprocessor}{#define NBASES 8}
 00006 \textcolor{preprocessor}{}\textcolor{comment}{/*@notnull@*/}
@@ -22,8 +23,8 @@
 00017  \{ 0, 0, 0, 0, 0, 1, 0, 0\},
 00018  \{ 0, 6, 0, 0, 5, 0, 0, 0\}\};
 00019 
-00020 \textcolor{preprocessor}{#define MAXALPHA 20       }\textcolor{comment}{/* maximal length of alphabet */}\textcolor{preprocessor}{}
-00021 \textcolor{preprocessor}{}
+00020 \textcolor{preprocessor}{#define MAXALPHA 20       }\textcolor{comment}{/* maximal length of alphabet */}
+00021 
 00022 \textcolor{keyword}{static} \textcolor{keywordtype}{short} alias[\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1];
 00023 \textcolor{keyword}{static} \textcolor{keywordtype}{int} pair[\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1][\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1];
 00024 \textcolor{comment}{/* rtype[pair[i][j]]:=pair[j][i] */}
@@ -88,18 +89,18 @@
 00083             alias[i++] = 3;  \textcolor{comment}{/* A <-> G */}
 00084             alias[i++] = 2;  \textcolor{comment}{/* B <-> C */}
 00085          \}
-00086          \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{
+00086          \textcolor{keywordflow}{for} (i=1; i<MAXALPHA; i++) \{
 00087             pair[i][i+1] = 2;    \textcolor{comment}{/* AB <-> GC */}
 00088             i++;
 00089             pair[i][i-1] = 1;    \textcolor{comment}{/* BA <-> CG */}
 00090          \}
 00091       \}
 00092       \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (energy\_set==2) \{
-00093         \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA};) \{
+00093         \textcolor{keywordflow}{for} (i=1; i<MAXALPHA;) \{
 00094             alias[i++] = 1;  \textcolor{comment}{/* A <-> A*/}
 00095             alias[i++] = 4;  \textcolor{comment}{/* B <-> U */}
 00096          \}
-00097          \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{
+00097          \textcolor{keywordflow}{for} (i=1; i<MAXALPHA; i++) \{
 00098             pair[i][i+1] = 5;    \textcolor{comment}{/* AB <-> AU */}
 00099             i++;
 00100             pair[i][i-1] = 6;    \textcolor{comment}{/* BA <-> UA */}
@@ -123,8 +124,8 @@
 00118         \}
 00119       \}
 00120       \textcolor{keywordflow}{else} \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror}(\textcolor{stringliteral}{"What energy\_set are YOU using??"});
-00121       \textcolor{keywordflow}{for} (i=0; i<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{
-00122         \textcolor{keywordflow}{for} (j=0; j<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; j++)
+00121       \textcolor{keywordflow}{for} (i=0; i<=MAXALPHA; i++) \{
+00122         \textcolor{keywordflow}{for} (j=0; j<=MAXALPHA; j++)
 00123           rtype[pair[i][j]] = pair[j][i];
 00124       \}
 00125    \}
@@ -151,4 +152,4 @@
 00146 
 00147   \textcolor{keywordflow}{return} S;
 00148 \}
-\end{DoxyCode}
+\end{alltt}\end{footnotesize}